Limits...
Phylogenetic Exploration of Nosocomial Transmission Chains of 2009 Influenza A/H1N1 among Children Admitted at Red Cross War Memorial Children's Hospital, Cape Town, South Africa in 2011.

Valley-Omar Z, Nindo F, Mudau M, Hsiao M, Martin DP - PLoS ONE (2015)

Bottom Line: These analyses suggested that most instances of potential hospital-acquired infections resulted from multiple introductions of Influenza A into the hospital, which included instances where virus hemagglutinin sequences were identical between different patients.In contrast, a traditional epidemiological investigation that used no viral phylogenetic analyses, based on patient co-admission into specific wards during a particular time-frame, suggested that multiple hospital acquired infection instances may have stemmed from a limited number of identifiable index viral isolates/patients.This traditional epidemiological analysis by itself could incorrectly suggest linkage between unrelated cases, underestimate the number of unique infections and may overlook the possible diffuse nature of hospital transmission, which was suggested by sequencing data to be caused by multiple unique introductions of influenza A isolates into individual hospital wards.

View Article: PubMed Central - PubMed

Affiliation: Centre for Respiratory Diseases and Meningitis, Virology, National Institute for Communicable Diseases, Sandringham, Johannesburg, South Africa.

ABSTRACT
Traditional modes of investigating influenza nosocomial transmission have entailed a combination of confirmatory molecular diagnostic testing and epidemiological investigation. Common hospital-acquired infections like influenza require a discerning ability to distinguish between viral isolates to accurately identify patient transmission chains. We assessed whether influenza hemagglutinin sequence phylogenies can be used to enrich epidemiological data when investigating the extent of nosocomial transmission over a four-month period within a paediatric Hospital in Cape Town South Africa. Possible transmission chains/channels were initially determined through basic patient admission data combined with Maximum likelihood and time-scaled Bayesian phylogenetic analyses. These analyses suggested that most instances of potential hospital-acquired infections resulted from multiple introductions of Influenza A into the hospital, which included instances where virus hemagglutinin sequences were identical between different patients. Furthermore, a general inability to establish epidemiological transmission linkage of patients/viral isolates implied that identified isolates could have originated from asymptomatic hospital patients, visitors or hospital staff. In contrast, a traditional epidemiological investigation that used no viral phylogenetic analyses, based on patient co-admission into specific wards during a particular time-frame, suggested that multiple hospital acquired infection instances may have stemmed from a limited number of identifiable index viral isolates/patients. This traditional epidemiological analysis by itself could incorrectly suggest linkage between unrelated cases, underestimate the number of unique infections and may overlook the possible diffuse nature of hospital transmission, which was suggested by sequencing data to be caused by multiple unique introductions of influenza A isolates into individual hospital wards. We have demonstrated a functional role for viral sequence data in nosocomial transmission investigation through its ability to enrich traditional, non-molecular observational epidemiological investigation by teasing out possible transmission pathways and working toward more accurately enumerating the number of possible transmission events.

Show MeSH

Related in: MedlinePlus

Time scaled maximum clade credibility (MCC) tree generated under GTR G + I and relaxed molecular clock in BEASTv1.7.5.The branch supports that are indicated are posterior probabilities (pp). Four significant putative transmission clusters containing sequences isolated from the study site (Red Cross Children’s Hospital and surrounding facilities) with pp support > 0.9 are highlighted in red.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4643913&req=5

pone.0141744.g003: Time scaled maximum clade credibility (MCC) tree generated under GTR G + I and relaxed molecular clock in BEASTv1.7.5.The branch supports that are indicated are posterior probabilities (pp). Four significant putative transmission clusters containing sequences isolated from the study site (Red Cross Children’s Hospital and surrounding facilities) with pp support > 0.9 are highlighted in red.

Mentions: To further explore the possibility that the four RXH clusters were the result of HAI, time-scaled Maximum Clade Credibility (MCC) phylogenies were constructed using BEAST. By the explicit inclusion of sampling times and estimated H1N1pdm evolutionary rates during the construction of the MCC tree, we were able to estimate the dates of the nodes in the tree. The dates of the root nodes of the four RXH clusters (and their 95% credibility intervals) were used to indicate whether they could plausibly have been the consequence of HAIs. Similar to the ML phylogenetic analysis, putative HAI transmission clusters were inferred if two or more sequences clustered with 0.95 or higher posterior probability support. Based on this criterion, exactly the same four RXH potential HAI transmission clusters were identified in the MCC tree (Fig 3) as were identified in the ML tree. Below we individually assess each of these clusters.


Phylogenetic Exploration of Nosocomial Transmission Chains of 2009 Influenza A/H1N1 among Children Admitted at Red Cross War Memorial Children's Hospital, Cape Town, South Africa in 2011.

Valley-Omar Z, Nindo F, Mudau M, Hsiao M, Martin DP - PLoS ONE (2015)

Time scaled maximum clade credibility (MCC) tree generated under GTR G + I and relaxed molecular clock in BEASTv1.7.5.The branch supports that are indicated are posterior probabilities (pp). Four significant putative transmission clusters containing sequences isolated from the study site (Red Cross Children’s Hospital and surrounding facilities) with pp support > 0.9 are highlighted in red.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4643913&req=5

pone.0141744.g003: Time scaled maximum clade credibility (MCC) tree generated under GTR G + I and relaxed molecular clock in BEASTv1.7.5.The branch supports that are indicated are posterior probabilities (pp). Four significant putative transmission clusters containing sequences isolated from the study site (Red Cross Children’s Hospital and surrounding facilities) with pp support > 0.9 are highlighted in red.
Mentions: To further explore the possibility that the four RXH clusters were the result of HAI, time-scaled Maximum Clade Credibility (MCC) phylogenies were constructed using BEAST. By the explicit inclusion of sampling times and estimated H1N1pdm evolutionary rates during the construction of the MCC tree, we were able to estimate the dates of the nodes in the tree. The dates of the root nodes of the four RXH clusters (and their 95% credibility intervals) were used to indicate whether they could plausibly have been the consequence of HAIs. Similar to the ML phylogenetic analysis, putative HAI transmission clusters were inferred if two or more sequences clustered with 0.95 or higher posterior probability support. Based on this criterion, exactly the same four RXH potential HAI transmission clusters were identified in the MCC tree (Fig 3) as were identified in the ML tree. Below we individually assess each of these clusters.

Bottom Line: These analyses suggested that most instances of potential hospital-acquired infections resulted from multiple introductions of Influenza A into the hospital, which included instances where virus hemagglutinin sequences were identical between different patients.In contrast, a traditional epidemiological investigation that used no viral phylogenetic analyses, based on patient co-admission into specific wards during a particular time-frame, suggested that multiple hospital acquired infection instances may have stemmed from a limited number of identifiable index viral isolates/patients.This traditional epidemiological analysis by itself could incorrectly suggest linkage between unrelated cases, underestimate the number of unique infections and may overlook the possible diffuse nature of hospital transmission, which was suggested by sequencing data to be caused by multiple unique introductions of influenza A isolates into individual hospital wards.

View Article: PubMed Central - PubMed

Affiliation: Centre for Respiratory Diseases and Meningitis, Virology, National Institute for Communicable Diseases, Sandringham, Johannesburg, South Africa.

ABSTRACT
Traditional modes of investigating influenza nosocomial transmission have entailed a combination of confirmatory molecular diagnostic testing and epidemiological investigation. Common hospital-acquired infections like influenza require a discerning ability to distinguish between viral isolates to accurately identify patient transmission chains. We assessed whether influenza hemagglutinin sequence phylogenies can be used to enrich epidemiological data when investigating the extent of nosocomial transmission over a four-month period within a paediatric Hospital in Cape Town South Africa. Possible transmission chains/channels were initially determined through basic patient admission data combined with Maximum likelihood and time-scaled Bayesian phylogenetic analyses. These analyses suggested that most instances of potential hospital-acquired infections resulted from multiple introductions of Influenza A into the hospital, which included instances where virus hemagglutinin sequences were identical between different patients. Furthermore, a general inability to establish epidemiological transmission linkage of patients/viral isolates implied that identified isolates could have originated from asymptomatic hospital patients, visitors or hospital staff. In contrast, a traditional epidemiological investigation that used no viral phylogenetic analyses, based on patient co-admission into specific wards during a particular time-frame, suggested that multiple hospital acquired infection instances may have stemmed from a limited number of identifiable index viral isolates/patients. This traditional epidemiological analysis by itself could incorrectly suggest linkage between unrelated cases, underestimate the number of unique infections and may overlook the possible diffuse nature of hospital transmission, which was suggested by sequencing data to be caused by multiple unique introductions of influenza A isolates into individual hospital wards. We have demonstrated a functional role for viral sequence data in nosocomial transmission investigation through its ability to enrich traditional, non-molecular observational epidemiological investigation by teasing out possible transmission pathways and working toward more accurately enumerating the number of possible transmission events.

Show MeSH
Related in: MedlinePlus