A high burden of asymptomatic gastrointestinal infections in traditional communities in Papua New Guinea
- Horwood, Paul, Soli, Kevin, Maure, Tobias, Naito, Yuichi, Morita, Ayako, Natsuhara, Kazumi, Tadokoro, Kiyoshi, Baba, Jun, Odani, Shingo, Tomitsuka, Eriko, Igai, Katsura, Larkins, Jo-Ann, Siba, Peter, Pomat, William, McBryde, Emma, Umezaki, Masahiro, Greenhill, Andrew
- Authors: Horwood, Paul , Soli, Kevin , Maure, Tobias , Naito, Yuichi , Morita, Ayako , Natsuhara, Kazumi , Tadokoro, Kiyoshi , Baba, Jun , Odani, Shingo , Tomitsuka, Eriko , Igai, Katsura , Larkins, Jo-Ann , Siba, Peter , Pomat, William , McBryde, Emma , Umezaki, Masahiro , Greenhill, Andrew
- Date: 2017
- Type: Text , Journal article
- Relation: American Journal of Tropical Medicine and Hygiene Vol. 97, no. 6 (2017), p. 1872-1875
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- Description: Stool samples were collected from 148 healthy adults living a traditional subsistence lifestyle in Papua New Guinea and screened for enteric pathogens using real-time RT-PCR/PCR assays. Enteric pathogens were detected in a high proportion (41%) of individuals. Clear differences were observed in the detection of pathogens between highland and lowland communities. In particular, there was a marked difference in detection rates of norovirus GII (20% and 0%, respectively) and Shigella sp. (15% and 0%, respectively). Analysis of the relationship between enteric pathogen carriage and microbial community composition of participants, using box plots to compare specific normal flora population numbers, did not suggest that gut microbial composition was directly associated with pathogen carriage. This study suggests that enteric pathogens are common in healthy individuals in Papua New Guinean highland communities, presumably acting as a reservoir of infection and thus contributing to a high burden of gastrointestinal illnesses.
- Authors: Horwood, Paul , Soli, Kevin , Maure, Tobias , Naito, Yuichi , Morita, Ayako , Natsuhara, Kazumi , Tadokoro, Kiyoshi , Baba, Jun , Odani, Shingo , Tomitsuka, Eriko , Igai, Katsura , Larkins, Jo-Ann , Siba, Peter , Pomat, William , McBryde, Emma , Umezaki, Masahiro , Greenhill, Andrew
- Date: 2017
- Type: Text , Journal article
- Relation: American Journal of Tropical Medicine and Hygiene Vol. 97, no. 6 (2017), p. 1872-1875
- Full Text:
- Reviewed:
- Description: Stool samples were collected from 148 healthy adults living a traditional subsistence lifestyle in Papua New Guinea and screened for enteric pathogens using real-time RT-PCR/PCR assays. Enteric pathogens were detected in a high proportion (41%) of individuals. Clear differences were observed in the detection of pathogens between highland and lowland communities. In particular, there was a marked difference in detection rates of norovirus GII (20% and 0%, respectively) and Shigella sp. (15% and 0%, respectively). Analysis of the relationship between enteric pathogen carriage and microbial community composition of participants, using box plots to compare specific normal flora population numbers, did not suggest that gut microbial composition was directly associated with pathogen carriage. This study suggests that enteric pathogens are common in healthy individuals in Papua New Guinean highland communities, presumably acting as a reservoir of infection and thus contributing to a high burden of gastrointestinal illnesses.
Antimicrobial sensitivity trends and virulence genes in Shigella spp. from the Oceania region
- Malau, Elisheba, Ford, Rebecca, Valcanis, Mary, Jennison, Amy, Mosse, Jenny, Bean, David, Yoannes, Mition, Pomat, William, Horwood, Paul, Greenhill, Andrew
- Authors: Malau, Elisheba , Ford, Rebecca , Valcanis, Mary , Jennison, Amy , Mosse, Jenny , Bean, David , Yoannes, Mition , Pomat, William , Horwood, Paul , Greenhill, Andrew
- Date: 2018
- Type: Text , Journal article
- Relation: Infection, Genetics and Evolution Vol. 64, no. (2018), p. 52-56
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- Description: Shigella is a common cause of diarrhoea in Papua New Guinea (PNG) and other Oceania countries. However, little is known about the strains causing infection. Archived Shigella isolates (n = 72) were obtained from research laboratories in PNG and reference laboratories in Australia. Shigella virulence genes were detected by PCR, and antimicrobial susceptibility was determined by disk diffusion. The ipaH virulence gene was present in all 72 isolates. The prevalence of other virulence genes was variable, with ial, invE, ipaBCD, sen/ospD3 and virF present in 60% of isolates and set1A and set1B genes present in 42% of isolates. Most S. flexneri isolates contained genes encoding enterotoxin 1 and/or enterotoxin 2. Resistance to antibiotics was common, with 51/72 isolates resistant to 2–4 antimicrobials. A greater proportion of bacteria isolated since 2010 (relative to pre-2010 isolates) were resistant to commonly used antibiotics such as ampicillin, chloramphenicol, tetracycline, and trimethoprim-sulfamethoxazole; suggesting that antimicrobial resistance (AMR) in Shigella is increasing over time in the Oceania region. There is a need for improved knowledge regarding Shigella circulation in the Oceania region and further monitoring of AMR patterns. © 2018 Elsevier B.V.
- Authors: Malau, Elisheba , Ford, Rebecca , Valcanis, Mary , Jennison, Amy , Mosse, Jenny , Bean, David , Yoannes, Mition , Pomat, William , Horwood, Paul , Greenhill, Andrew
- Date: 2018
- Type: Text , Journal article
- Relation: Infection, Genetics and Evolution Vol. 64, no. (2018), p. 52-56
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- Description: Shigella is a common cause of diarrhoea in Papua New Guinea (PNG) and other Oceania countries. However, little is known about the strains causing infection. Archived Shigella isolates (n = 72) were obtained from research laboratories in PNG and reference laboratories in Australia. Shigella virulence genes were detected by PCR, and antimicrobial susceptibility was determined by disk diffusion. The ipaH virulence gene was present in all 72 isolates. The prevalence of other virulence genes was variable, with ial, invE, ipaBCD, sen/ospD3 and virF present in 60% of isolates and set1A and set1B genes present in 42% of isolates. Most S. flexneri isolates contained genes encoding enterotoxin 1 and/or enterotoxin 2. Resistance to antibiotics was common, with 51/72 isolates resistant to 2–4 antimicrobials. A greater proportion of bacteria isolated since 2010 (relative to pre-2010 isolates) were resistant to commonly used antibiotics such as ampicillin, chloramphenicol, tetracycline, and trimethoprim-sulfamethoxazole; suggesting that antimicrobial resistance (AMR) in Shigella is increasing over time in the Oceania region. There is a need for improved knowledge regarding Shigella circulation in the Oceania region and further monitoring of AMR patterns. © 2018 Elsevier B.V.
Divergent Barmah forest virus from Papua New Guinea
- Caly, Leon, Horwood, Paul, Dhanasekaran, VijaykrishnaLynch, Stacey, Greenhill, Andrew, Pomat, William, Rai, Glennis, Kisa, Debbie, Bande, Grace, Druce, Julian, Abdad, Mohammad
- Authors: Caly, Leon , Horwood, Paul , Dhanasekaran, VijaykrishnaLynch, Stacey , Greenhill, Andrew , Pomat, William , Rai, Glennis , Kisa, Debbie , Bande, Grace , Druce, Julian , Abdad, Mohammad
- Date: 2019
- Type: Text , Journal article
- Relation: Emerging Infectious Diseases Vol. 25, no. 12 (2019), p. 2266-2269
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- Description: We report a case of Barmah Forest virus infection in a child from Central Province, Papua New Guinea, who had no previous travel history. Genomic characterization of the virus showed divergent origin compared with viruses previously detected, supporting the hypothesis that the range of Barmah Forest virus extends beyond Australia. © 2019 Centers for Disease Control and Prevention (CDC). All rights reserved.
- Authors: Caly, Leon , Horwood, Paul , Dhanasekaran, VijaykrishnaLynch, Stacey , Greenhill, Andrew , Pomat, William , Rai, Glennis , Kisa, Debbie , Bande, Grace , Druce, Julian , Abdad, Mohammad
- Date: 2019
- Type: Text , Journal article
- Relation: Emerging Infectious Diseases Vol. 25, no. 12 (2019), p. 2266-2269
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- Description: We report a case of Barmah Forest virus infection in a child from Central Province, Papua New Guinea, who had no previous travel history. Genomic characterization of the virus showed divergent origin compared with viruses previously detected, supporting the hypothesis that the range of Barmah Forest virus extends beyond Australia. © 2019 Centers for Disease Control and Prevention (CDC). All rights reserved.
Gut microbiota composition in obese and non-obese adult relatives from the highlands of Papua New Guinea
- Jonduo, Marinjho, Wawae, Lorry, Masiria, Geraldine, Suda, Wataru, Hattori, Masahira, Takayasu, Lena, Abdad, Mohammad, Greenhill, Andrew, Horwood, Paul, Pomat, William, Umezaki, Masahiro
- Authors: Jonduo, Marinjho , Wawae, Lorry , Masiria, Geraldine , Suda, Wataru , Hattori, Masahira , Takayasu, Lena , Abdad, Mohammad , Greenhill, Andrew , Horwood, Paul , Pomat, William , Umezaki, Masahiro
- Date: 2020
- Type: Text , Journal article
- Relation: FEMS microbiology letters Vol. 367, no. 19 (2020), p.
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- Description: Obesity is a condition that results from an imbalance between energy intake and expenditure. Recently, obesity has been linked to differences in the composition of gut microbiota. To examine this association in Papua New Guinea (PNG) highlanders, fecal samples were collected from 18 adults; nine obese participants were paired with their non-obese relative. Amplification of the 16S rRNA gene targeting the V1-V2 region was performed on DNA extracts for each participant, with high-quality sequences selected and used for operational taxonomic unit clustering. The data showed Firmicutes and Bacteroidetes were the two dominant phyla, while at genus level Prevotella was the most dominant genus in all of the samples. Nonetheless, statistical evaluation of potential association between nutritional status and bacterial abundance at both phyla and genus levels showed no significant difference. Further studies, ideally in both rural and urban areas, are needed to evaluate the role of the gut microbiome in the occurrence of obesity in PNG and other resource-limited settings. © The Author(s) 2020. Published by Oxford University Press on behalf of FEMS.
- Authors: Jonduo, Marinjho , Wawae, Lorry , Masiria, Geraldine , Suda, Wataru , Hattori, Masahira , Takayasu, Lena , Abdad, Mohammad , Greenhill, Andrew , Horwood, Paul , Pomat, William , Umezaki, Masahiro
- Date: 2020
- Type: Text , Journal article
- Relation: FEMS microbiology letters Vol. 367, no. 19 (2020), p.
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- Description: Obesity is a condition that results from an imbalance between energy intake and expenditure. Recently, obesity has been linked to differences in the composition of gut microbiota. To examine this association in Papua New Guinea (PNG) highlanders, fecal samples were collected from 18 adults; nine obese participants were paired with their non-obese relative. Amplification of the 16S rRNA gene targeting the V1-V2 region was performed on DNA extracts for each participant, with high-quality sequences selected and used for operational taxonomic unit clustering. The data showed Firmicutes and Bacteroidetes were the two dominant phyla, while at genus level Prevotella was the most dominant genus in all of the samples. Nonetheless, statistical evaluation of potential association between nutritional status and bacterial abundance at both phyla and genus levels showed no significant difference. Further studies, ideally in both rural and urban areas, are needed to evaluate the role of the gut microbiome in the occurrence of obesity in PNG and other resource-limited settings. © The Author(s) 2020. Published by Oxford University Press on behalf of FEMS.
Phylodynamic signatures in the emergence of community-associated MRSA
- Steinig, Eike, Aglua, Izzard, Duchene, Sebastian, Meehan, Michael, Yoannes, Mition, Firth, Cadhla, Jaworski, Jan, Drekore, Jimmy, Urakoko, Bohu, Poka, Harry, Wurr, Clive, Ebos, Eri, Nangen, David, Müller, Elke, Mulvey, Peter, Jackson, Charlene, Blomfeldt, Anita, Aamot, Hege, Laman, Moses, Manning, Laurens, Earls, Megan, Coleman, David, Greenhill, Andrew, Ford, Rebecca, Stegger, Marc, Syed, Muhammad, Jamil, Bushra, Monecke, Stefan, Ehricht, Ralf, Smith, Simon, Pomat, William, Horwood, Paul, Tong, Steven, McBryde, Emma
- Authors: Steinig, Eike , Aglua, Izzard , Duchene, Sebastian , Meehan, Michael , Yoannes, Mition , Firth, Cadhla , Jaworski, Jan , Drekore, Jimmy , Urakoko, Bohu , Poka, Harry , Wurr, Clive , Ebos, Eri , Nangen, David , Müller, Elke , Mulvey, Peter , Jackson, Charlene , Blomfeldt, Anita , Aamot, Hege , Laman, Moses , Manning, Laurens , Earls, Megan , Coleman, David , Greenhill, Andrew , Ford, Rebecca , Stegger, Marc , Syed, Muhammad , Jamil, Bushra , Monecke, Stefan , Ehricht, Ralf , Smith, Simon , Pomat, William , Horwood, Paul , Tong, Steven , McBryde, Emma
- Date: 2022
- Type: Text , Journal article
- Relation: Proceedings of the National Academy of Sciences of the United States of America Vol. 119, no. 45 (2022), p.
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- Description: Community-associated, methicillin-resistant Staphylococcus aureus (MRSA) lineages have emerged in many geographically distinct regions around the world during the past 30 y. Here, we apply consistent phylodynamic methods across multiple community-associated MRSA lineages to describe and contrast their patterns of emergence and dissemination. We generated whole-genome sequencing data for the Australian sequence type (ST) ST93-MRSA-IV from remote communities in Far North Queensland and Papua New Guinea, and the Bengal Bay ST772-MRSA-V clone from metropolitan communities in Pakistan. Increases in the effective reproduction number (Re) and sustained transmission (Re > 1) coincided with spread of progenitor methicillin-susceptible S. aureus (MSSA) in remote northern Australian populations, dissemination of the ST93-MRSA-IV genotype into population centers on the Australian East Coast, and subsequent importation into the highlands of Papua New Guinea and Far North Queensland. Applying the same phylodynamic methods to existing lineage datasets, we identified common signatures of epidemic growth in the emergence and epidemiological trajectory of community-associated S. aureus lineages from America, Asia, Australasia, and Europe. Surges in Re were observed at the divergence of antibiotic-resistant strains, coinciding with their establishment in regional population centers. Epidemic growth was also observed among drug-resistant MSSA clades in Africa and northern Australia. Our data suggest that the emergence of community-associated MRSA in the late 20th century was driven by a combination of antibiotic-resistant genotypes and host epidemiology, leading to abrupt changes in lineage-wide transmission dynamics and sustained transmission in regional population centers. Copyright © 2022 the Author(s).
- Authors: Steinig, Eike , Aglua, Izzard , Duchene, Sebastian , Meehan, Michael , Yoannes, Mition , Firth, Cadhla , Jaworski, Jan , Drekore, Jimmy , Urakoko, Bohu , Poka, Harry , Wurr, Clive , Ebos, Eri , Nangen, David , Müller, Elke , Mulvey, Peter , Jackson, Charlene , Blomfeldt, Anita , Aamot, Hege , Laman, Moses , Manning, Laurens , Earls, Megan , Coleman, David , Greenhill, Andrew , Ford, Rebecca , Stegger, Marc , Syed, Muhammad , Jamil, Bushra , Monecke, Stefan , Ehricht, Ralf , Smith, Simon , Pomat, William , Horwood, Paul , Tong, Steven , McBryde, Emma
- Date: 2022
- Type: Text , Journal article
- Relation: Proceedings of the National Academy of Sciences of the United States of America Vol. 119, no. 45 (2022), p.
- Full Text:
- Reviewed:
- Description: Community-associated, methicillin-resistant Staphylococcus aureus (MRSA) lineages have emerged in many geographically distinct regions around the world during the past 30 y. Here, we apply consistent phylodynamic methods across multiple community-associated MRSA lineages to describe and contrast their patterns of emergence and dissemination. We generated whole-genome sequencing data for the Australian sequence type (ST) ST93-MRSA-IV from remote communities in Far North Queensland and Papua New Guinea, and the Bengal Bay ST772-MRSA-V clone from metropolitan communities in Pakistan. Increases in the effective reproduction number (Re) and sustained transmission (Re > 1) coincided with spread of progenitor methicillin-susceptible S. aureus (MSSA) in remote northern Australian populations, dissemination of the ST93-MRSA-IV genotype into population centers on the Australian East Coast, and subsequent importation into the highlands of Papua New Guinea and Far North Queensland. Applying the same phylodynamic methods to existing lineage datasets, we identified common signatures of epidemic growth in the emergence and epidemiological trajectory of community-associated S. aureus lineages from America, Asia, Australasia, and Europe. Surges in Re were observed at the divergence of antibiotic-resistant strains, coinciding with their establishment in regional population centers. Epidemic growth was also observed among drug-resistant MSSA clades in Africa and northern Australia. Our data suggest that the emergence of community-associated MRSA in the late 20th century was driven by a combination of antibiotic-resistant genotypes and host epidemiology, leading to abrupt changes in lineage-wide transmission dynamics and sustained transmission in regional population centers. Copyright © 2022 the Author(s).
Whole genome sequence analysis of Salmonella Typhi in Papua New Guinea reveals an established population of genotype 2.1.7 sensitive to antimicrobials
- Dyson, Zoe, Malau, Elisheba, Horwood, Paul, Ford, Rebecca, Siba, Valentine, Yoannes, Mition, Pomat, William, Passey, Megan, Judd, Louise, Ingle, Danielle, Williamson, Deborah, Dougan, Gordon, Greenhill, Andrew, Holt, Kathryn
- Authors: Dyson, Zoe , Malau, Elisheba , Horwood, Paul , Ford, Rebecca , Siba, Valentine , Yoannes, Mition , Pomat, William , Passey, Megan , Judd, Louise , Ingle, Danielle , Williamson, Deborah , Dougan, Gordon , Greenhill, Andrew , Holt, Kathryn
- Date: 2022
- Type: Text , Journal article
- Relation: PLoS Neglected Tropical Diseases Vol. 16, no. 3 (2022), p.
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- Description: Background Typhoid fever, a systemic infection caused by Salmonella enterica serovar Typhi, remains a considerable public health threat in impoverished regions within many low-and middle-income settings. However, we still lack a detailed understanding of the emergence, population structure, molecular mechanisms of antimicrobial resistance (AMR), and transmission dynamics of S. Typhi across many settings, particularly throughout the Asia-Pacific islands. Here we present a comprehensive whole genome sequence (WGS) based overview of S. Typhi populations circulating in Papua New Guinea (PNG) over 30 years. Principle findings Bioinformatic analysis of 86 S. Typhi isolates collected between 1980–2010 demonstrated that the population structure of PNG is dominated by a single genotype (2.1.7) that appears to have emerged in the Indonesian archipelago in the mid-twentieth century with minimal evidence of inter-country transmission. Genotypic and phenotypic data demonstrated that the PNG S. Typhi population appears to be susceptible to former first line drugs for treating typhoid fever (chloramphenicol, ampicillin and co-trimoxazole), as well as fluoroquinolones, third generation cephalosporins, and macrolides. PNG genotype 2.1.7 was genetically con-served, with very few deletions, and no evidence of plasmid or prophage acquisition. Genetic variation among this population was attributed to either single point mutations, or homologous recombination adjacent to repetitive ribosomal RNA operons. Significance Antimicrobials remain an effective option for the treatment of typhoid fever in PNG, along with other intervention strategies including improvements to water, sanitation and hygiene (WaSH) related infrastructure and potentially the introduction of Vi-conjugate vaccines. However, continued genomic surveillance is warranted to monitor for the emergence of AMR within local populations, or the introduction of AMR associated genotypes of S. Typhi in this setting. © The Authors.
- Authors: Dyson, Zoe , Malau, Elisheba , Horwood, Paul , Ford, Rebecca , Siba, Valentine , Yoannes, Mition , Pomat, William , Passey, Megan , Judd, Louise , Ingle, Danielle , Williamson, Deborah , Dougan, Gordon , Greenhill, Andrew , Holt, Kathryn
- Date: 2022
- Type: Text , Journal article
- Relation: PLoS Neglected Tropical Diseases Vol. 16, no. 3 (2022), p.
- Full Text:
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- Description: Background Typhoid fever, a systemic infection caused by Salmonella enterica serovar Typhi, remains a considerable public health threat in impoverished regions within many low-and middle-income settings. However, we still lack a detailed understanding of the emergence, population structure, molecular mechanisms of antimicrobial resistance (AMR), and transmission dynamics of S. Typhi across many settings, particularly throughout the Asia-Pacific islands. Here we present a comprehensive whole genome sequence (WGS) based overview of S. Typhi populations circulating in Papua New Guinea (PNG) over 30 years. Principle findings Bioinformatic analysis of 86 S. Typhi isolates collected between 1980–2010 demonstrated that the population structure of PNG is dominated by a single genotype (2.1.7) that appears to have emerged in the Indonesian archipelago in the mid-twentieth century with minimal evidence of inter-country transmission. Genotypic and phenotypic data demonstrated that the PNG S. Typhi population appears to be susceptible to former first line drugs for treating typhoid fever (chloramphenicol, ampicillin and co-trimoxazole), as well as fluoroquinolones, third generation cephalosporins, and macrolides. PNG genotype 2.1.7 was genetically con-served, with very few deletions, and no evidence of plasmid or prophage acquisition. Genetic variation among this population was attributed to either single point mutations, or homologous recombination adjacent to repetitive ribosomal RNA operons. Significance Antimicrobials remain an effective option for the treatment of typhoid fever in PNG, along with other intervention strategies including improvements to water, sanitation and hygiene (WaSH) related infrastructure and potentially the introduction of Vi-conjugate vaccines. However, continued genomic surveillance is warranted to monitor for the emergence of AMR within local populations, or the introduction of AMR associated genotypes of S. Typhi in this setting. © The Authors.
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