The molecular epidemiology of influenza in Cambodia
- Authors: Suttie, Annika
- Date: 2019
- Type: Text , Thesis , PhD
- Full Text:
- Description: Avian influenza viruses (AIVs) represent a risk to the health of humans and animals. The prevalence of AIVs in live bird markets in Cambodia is among the highest in the world, being detected in 45.5% of tested poultry in 2015. To better understand the potential risk presented by AIVs, this thesis investigated the genetic characteristics of AIVs circulating in Cambodia between 2014 to 2018; focusing on subtypes that pose the greatest risk to human and animal health (H5, H7 and H9). Highly pathogenic (HP) H5N1 clade 2.3.2.1c viruses and low pathogenic H9N2 BJ/94-like h9-4.2.5 clade viruses were the most frequently detected subtypes, and circulate endemically in Cambodia’s domestic poultry. Co-infections were detected and facilitated the production of two novel reassortant H5N1 AIVs with single genes from H9N2 viruses. Additionally, numerous intrasubtypic reassortment events were detected for H5 and H9 AIVs. This is concerning as reassortment events can rapidly produce novel viruses of public health risk. Phylogenetic analyses showed some genes of the Cambodian H5, H7 and H9 AIVs clustered with zoonotic viruses, suggesting a common origin. There are parallels between H5N1 and H9N2 AIVs detected in Cambodia and Vietnam, likely facilitated through the illegal trade of live poultry and/or the migration of wild birds. Molecular analyses showed H9 AIVs have major markers associated with adaptation to mammals; though during the study period the only human AIV cases were the result of HP H5N1. Molecular markers of resistance to adamantine antivirals was observed in 3% of H5 and 41% of H9 AIVs; however, both subtypes remain susceptible to first line antiviral treatment, neuraminidase inhibitors. The data presented in this thesis demonstrates that circulation of Cambodian AIVs represents a risk for the emergence of novel viruses. Interventions are urgently needed to mitigate the threat posed to poultry and humans.
- Description: Doctor of Philosophy
- Authors: Suttie, Annika
- Date: 2019
- Type: Text , Thesis , PhD
- Full Text:
- Description: Avian influenza viruses (AIVs) represent a risk to the health of humans and animals. The prevalence of AIVs in live bird markets in Cambodia is among the highest in the world, being detected in 45.5% of tested poultry in 2015. To better understand the potential risk presented by AIVs, this thesis investigated the genetic characteristics of AIVs circulating in Cambodia between 2014 to 2018; focusing on subtypes that pose the greatest risk to human and animal health (H5, H7 and H9). Highly pathogenic (HP) H5N1 clade 2.3.2.1c viruses and low pathogenic H9N2 BJ/94-like h9-4.2.5 clade viruses were the most frequently detected subtypes, and circulate endemically in Cambodia’s domestic poultry. Co-infections were detected and facilitated the production of two novel reassortant H5N1 AIVs with single genes from H9N2 viruses. Additionally, numerous intrasubtypic reassortment events were detected for H5 and H9 AIVs. This is concerning as reassortment events can rapidly produce novel viruses of public health risk. Phylogenetic analyses showed some genes of the Cambodian H5, H7 and H9 AIVs clustered with zoonotic viruses, suggesting a common origin. There are parallels between H5N1 and H9N2 AIVs detected in Cambodia and Vietnam, likely facilitated through the illegal trade of live poultry and/or the migration of wild birds. Molecular analyses showed H9 AIVs have major markers associated with adaptation to mammals; though during the study period the only human AIV cases were the result of HP H5N1. Molecular markers of resistance to adamantine antivirals was observed in 3% of H5 and 41% of H9 AIVs; however, both subtypes remain susceptible to first line antiviral treatment, neuraminidase inhibitors. The data presented in this thesis demonstrates that circulation of Cambodian AIVs represents a risk for the emergence of novel viruses. Interventions are urgently needed to mitigate the threat posed to poultry and humans.
- Description: Doctor of Philosophy
Co-circulation of influenza A H5, H7, and H9 viruses and co-infected poultry in live bird markets, Cambodia
- Horwood, Paul, Horm, Srey, Suttie, Annika, Thet, Sopheak, Rith, Phalla, Sorn, San, Holl, Davun, Tum, Sothyra, Ly, Sowath, Karlsson, Erik, Tarantola, Arnaud, Dussart, Philippe
- Authors: Horwood, Paul , Horm, Srey , Suttie, Annika , Thet, Sopheak , Rith, Phalla , Sorn, San , Holl, Davun , Tum, Sothyra , Ly, Sowath , Karlsson, Erik , Tarantola, Arnaud , Dussart, Philippe
- Date: 2018
- Type: Text , Journal article
- Relation: Emerging Infectious Diseases Vol. 24, no. 2 (2018), p. 352-355
- Full Text:
- Reviewed:
- Description: Longitudinal surveillance of 2 live bird markets in Cambodia revealed year-round, high co-circulation of H5, H7, and H9 influenza viruses. We detected influenza A viruses in 51.3% of ducks and 39.6% of chickens, and co-infections, mainly by H5 and H9 viruses, in 0.8% of ducks and 4.5% of chickens. © 2018 Centers for Disease Control and Prevention (CDC). All rights Reserved.
- Authors: Horwood, Paul , Horm, Srey , Suttie, Annika , Thet, Sopheak , Rith, Phalla , Sorn, San , Holl, Davun , Tum, Sothyra , Ly, Sowath , Karlsson, Erik , Tarantola, Arnaud , Dussart, Philippe
- Date: 2018
- Type: Text , Journal article
- Relation: Emerging Infectious Diseases Vol. 24, no. 2 (2018), p. 352-355
- Full Text:
- Reviewed:
- Description: Longitudinal surveillance of 2 live bird markets in Cambodia revealed year-round, high co-circulation of H5, H7, and H9 influenza viruses. We detected influenza A viruses in 51.3% of ducks and 39.6% of chickens, and co-infections, mainly by H5 and H9 viruses, in 0.8% of ducks and 4.5% of chickens. © 2018 Centers for Disease Control and Prevention (CDC). All rights Reserved.
Polymyxin resistant bacteria in Australian poultry
- Bean, David, Wigmore, Sarah, Abdul Momin, Muhd, Wareham, David
- Authors: Bean, David , Wigmore, Sarah , Abdul Momin, Muhd , Wareham, David
- Date: 2020
- Type: Text , Journal article
- Relation: Frontiers in Sustainable Food Systems Vol. 4, no. (2020), p. 1-7
- Full Text:
- Reviewed:
- Description: Resistance to last-resort antibiotics is significant public health issue. Antibiotic use in animal husbandry may be a driver of resistance that can subsequently be disseminated via the food chain. This study sought to determine the level of polymyxin resistance in Gram-negative pathogens present in Australian poultry, particularly the presence of mobilizable mechanisms of polymyxin resistance. Cloacal swabs from 213 birds were taken in a point prevalence survey from six different farms at a Victorian chicken processing facility. Colistin resistant organisms were recovered by direct plating on CHROMagar COL-APSE media. Bacterial isolates were identified and analyzed by MALDI-TOF, biochemical and genotypic assays. The 213 specimens yielded 57 (26.8%) colistin-resistant Gram-negative organisms, all of which have been previously described as exhibiting intrinsic resistance to polymyxin antibiotics. The most frequent organism was identified as Hafnia paralvei (40/57; 70%). Other colistin-resistant organisms included Aeromonas hydrophila (16%), Myroides odoratus (7%), Alcaligenes faecalis (5%), and Pseudochrobactrum spp. (2%). No mobile colistin resistance (mcr) genes were detected, although the arnA gene was identified in two A. hydrophila isolates and may mediate colistin resistance in these isolates. Intrinsic polymyxin-resistant organisms are widely distributed in the food chain, with over a quarter of the birds tested yielding a polymyxin-resistant organism. However, strains containing mcr genes remain rare in Australian poultry. © Copyright © 2020 Bean, Wigmore, Abdul Momin and Wareham.
- Authors: Bean, David , Wigmore, Sarah , Abdul Momin, Muhd , Wareham, David
- Date: 2020
- Type: Text , Journal article
- Relation: Frontiers in Sustainable Food Systems Vol. 4, no. (2020), p. 1-7
- Full Text:
- Reviewed:
- Description: Resistance to last-resort antibiotics is significant public health issue. Antibiotic use in animal husbandry may be a driver of resistance that can subsequently be disseminated via the food chain. This study sought to determine the level of polymyxin resistance in Gram-negative pathogens present in Australian poultry, particularly the presence of mobilizable mechanisms of polymyxin resistance. Cloacal swabs from 213 birds were taken in a point prevalence survey from six different farms at a Victorian chicken processing facility. Colistin resistant organisms were recovered by direct plating on CHROMagar COL-APSE media. Bacterial isolates were identified and analyzed by MALDI-TOF, biochemical and genotypic assays. The 213 specimens yielded 57 (26.8%) colistin-resistant Gram-negative organisms, all of which have been previously described as exhibiting intrinsic resistance to polymyxin antibiotics. The most frequent organism was identified as Hafnia paralvei (40/57; 70%). Other colistin-resistant organisms included Aeromonas hydrophila (16%), Myroides odoratus (7%), Alcaligenes faecalis (5%), and Pseudochrobactrum spp. (2%). No mobile colistin resistance (mcr) genes were detected, although the arnA gene was identified in two A. hydrophila isolates and may mediate colistin resistance in these isolates. Intrinsic polymyxin-resistant organisms are widely distributed in the food chain, with over a quarter of the birds tested yielding a polymyxin-resistant organism. However, strains containing mcr genes remain rare in Australian poultry. © Copyright © 2020 Bean, Wigmore, Abdul Momin and Wareham.
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