The influences of low protein diet on the intestinal microbiota of mice
- Masuoka, Hiroaki, Suda, Wataru, Tomitsuka, Eriko, Shindo, Chie, Takayasu, Lena, Horwood, Paul, Greenhill, Andrew, Hattori, Masahira, Umezaki, Masahiro, Hirayama, Kazuhiro
- Authors: Masuoka, Hiroaki , Suda, Wataru , Tomitsuka, Eriko , Shindo, Chie , Takayasu, Lena , Horwood, Paul , Greenhill, Andrew , Hattori, Masahira , Umezaki, Masahiro , Hirayama, Kazuhiro
- Date: 2020
- Type: Text , Journal article
- Relation: Scientific Reports Vol. 10, no. 1 (2020), p.
- Full Text:
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- Description: Recent research suggests that protein deficiency symptoms are influenced by the intestinal microbiota. We investigated the influence of low protein diet on composition of the intestinal microbiota through animal experiments. Specific pathogen-free (SPF) mice were fed one of four diets (3, 6, 9, or 12% protein) for 4 weeks (n = 5 per diet). Mice fed the 3% protein diet showed protein deficiency symptoms such as weight loss and low level of blood urea nitrogen concentration in their serum. The intestinal microbiota of mice in the 3% and 12% protein diet groups at day 0, 7, 14, 21 and 28 were investigated by 16S rRNA gene sequencing, which revealed differences in the microbiota. In the 3% protein diet group, a greater abundance of urease producing bacterial species was detected across the duration of the study. In the 12% diet protein group, increases of abundance of Streptococcaceae and Clostridiales families was detected. These results suggest that protein deficiency may be associated with shifts in intestinal microbiota. © 2020, The Author(s).
- Authors: Masuoka, Hiroaki , Suda, Wataru , Tomitsuka, Eriko , Shindo, Chie , Takayasu, Lena , Horwood, Paul , Greenhill, Andrew , Hattori, Masahira , Umezaki, Masahiro , Hirayama, Kazuhiro
- Date: 2020
- Type: Text , Journal article
- Relation: Scientific Reports Vol. 10, no. 1 (2020), p.
- Full Text:
- Reviewed:
- Description: Recent research suggests that protein deficiency symptoms are influenced by the intestinal microbiota. We investigated the influence of low protein diet on composition of the intestinal microbiota through animal experiments. Specific pathogen-free (SPF) mice were fed one of four diets (3, 6, 9, or 12% protein) for 4 weeks (n = 5 per diet). Mice fed the 3% protein diet showed protein deficiency symptoms such as weight loss and low level of blood urea nitrogen concentration in their serum. The intestinal microbiota of mice in the 3% and 12% protein diet groups at day 0, 7, 14, 21 and 28 were investigated by 16S rRNA gene sequencing, which revealed differences in the microbiota. In the 3% protein diet group, a greater abundance of urease producing bacterial species was detected across the duration of the study. In the 12% diet protein group, increases of abundance of Streptococcaceae and Clostridiales families was detected. These results suggest that protein deficiency may be associated with shifts in intestinal microbiota. © 2020, The Author(s).
Streptococcus pneumoniae and Haemophilus influenzae in paediatric meningitis patients at Goroka General Hospital, Papua New Guinea : Serotype distribution and antimicrobial susceptibility in the pre-vaccine era
- Greenhill, Andrew, Phuanukoonnon, Suparat, Michael, Audrey, Yoannes, Mition, Orami, Tilda, Smith, Helen, Murphy, Denise, Blyth, Christopher, Reeder, John, Siba, Peter, Pomat, William, Lehmann, Deborah
- Authors: Greenhill, Andrew , Phuanukoonnon, Suparat , Michael, Audrey , Yoannes, Mition , Orami, Tilda , Smith, Helen , Murphy, Denise , Blyth, Christopher , Reeder, John , Siba, Peter , Pomat, William , Lehmann, Deborah
- Date: 2015
- Type: Text , Journal article
- Relation: BMC Infectious Diseases Vol. 15, no. 485 (2015), p. 1-8
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- Description: Background: Bacterial meningitis remains an important infection globally, with the greatest burden in children in low-income settings, including Papua New Guinea (PNG). We present serotype, antimicrobial susceptibility and outcome data from paediatric meningitis patients prior to introduction of Haemophilus influenzae type b (Hib) and pneumococcal conjugate vaccines (PCVs) in PNG, providing a baseline for evaluation of immunisation programs. Methods: Cerebrospinal fluid (CSF) was collected from children admitted to Goroka General Hospital with suspected meningitis between 1996 and 2005. Culture and sensitivity was conducted, and pneumococci and H. influenzae were serotyped. Laboratory findings were linked to clinical outcomes. Results: We enrolled 1884 children. A recognised pathogen was identified in 375 children (19.9%). Streptococcus pneumoniae (n = 180) and Hib (n = 153) accounted for 88.8% of pathogens isolated. 24 different pneumococcal serogroups were identified; non-PCV types 2, 24 and 46 accounted for 31.6% of pneumococcal meningitis. 10- and 13-valent PCVs would cover 44.1% and 45.4% of pneumococcal meningitis respectively. Pneumococcal isolates were commonly resistant to penicillin (21.5%) and 23% of Hib isolates were simultaneously resistant to ampicillin, co-trimoxazole and chloramphenicol. The case fatality rate in patients with a recognised bacterial pathogen was 13.4% compared to 8.5% in culture-negative patients. Conclusions: If implemented in routine expanded programme of immunisation (EPI) with high coverage, current PCVs could prevent almost half of pneumococcal meningitis cases. Given the diversity of circulating serotypes in PNG serotype replacement is of concern. Ongoing surveillance is imperative to monitor the impact of vaccines. In the longer term vaccines providing broader protection against pneumococcal meningitis will be needed. © 2015 Greenhill et al.
- Authors: Greenhill, Andrew , Phuanukoonnon, Suparat , Michael, Audrey , Yoannes, Mition , Orami, Tilda , Smith, Helen , Murphy, Denise , Blyth, Christopher , Reeder, John , Siba, Peter , Pomat, William , Lehmann, Deborah
- Date: 2015
- Type: Text , Journal article
- Relation: BMC Infectious Diseases Vol. 15, no. 485 (2015), p. 1-8
- Full Text:
- Reviewed:
- Description: Background: Bacterial meningitis remains an important infection globally, with the greatest burden in children in low-income settings, including Papua New Guinea (PNG). We present serotype, antimicrobial susceptibility and outcome data from paediatric meningitis patients prior to introduction of Haemophilus influenzae type b (Hib) and pneumococcal conjugate vaccines (PCVs) in PNG, providing a baseline for evaluation of immunisation programs. Methods: Cerebrospinal fluid (CSF) was collected from children admitted to Goroka General Hospital with suspected meningitis between 1996 and 2005. Culture and sensitivity was conducted, and pneumococci and H. influenzae were serotyped. Laboratory findings were linked to clinical outcomes. Results: We enrolled 1884 children. A recognised pathogen was identified in 375 children (19.9%). Streptococcus pneumoniae (n = 180) and Hib (n = 153) accounted for 88.8% of pathogens isolated. 24 different pneumococcal serogroups were identified; non-PCV types 2, 24 and 46 accounted for 31.6% of pneumococcal meningitis. 10- and 13-valent PCVs would cover 44.1% and 45.4% of pneumococcal meningitis respectively. Pneumococcal isolates were commonly resistant to penicillin (21.5%) and 23% of Hib isolates were simultaneously resistant to ampicillin, co-trimoxazole and chloramphenicol. The case fatality rate in patients with a recognised bacterial pathogen was 13.4% compared to 8.5% in culture-negative patients. Conclusions: If implemented in routine expanded programme of immunisation (EPI) with high coverage, current PCVs could prevent almost half of pneumococcal meningitis cases. Given the diversity of circulating serotypes in PNG serotype replacement is of concern. Ongoing surveillance is imperative to monitor the impact of vaccines. In the longer term vaccines providing broader protection against pneumococcal meningitis will be needed. © 2015 Greenhill et al.
The Gut Microbiota of Rural Papua New Guineans : Composition, Diversity Patterns, and Ecological Processes
- Martínez, Inés, Stegen, James, Maldonado-Gómez, Maria, Eren, Murat, Siba, Peter, Greenhill, Andrew, Walter, Jens
- Authors: Martínez, Inés , Stegen, James , Maldonado-Gómez, Maria , Eren, Murat , Siba, Peter , Greenhill, Andrew , Walter, Jens
- Date: 2015
- Type: Text , Journal article
- Relation: Cell Reports Vol. 11, no. 4 (2015), p. 527-538
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- Description: Although recent research revealed an impact of westernization on diversity and composition of the human gut microbiota, the exact consequences on metacommunity characteristics are insufficiently understood, and the underlying ecological mechanisms have not been elucidated. Here, we have compared the fecal microbiota of adults from two non-industrialized regions in Papua New Guinea (PNG) with that of United States (US) residents. Papua New Guineans harbor communities with greater bacterial diversity, lower inter-individual variation, vastly different abundance profiles, and bacterial lineages undetectable in US residents. A quantification of the ecological processes that govern community assembly identified bacterial dispersal as the dominant process that shapes the microbiome in PNG but not in the US. These findings suggest that the microbiome alterations detected in industrialized societies might arise from modern lifestyle factors limiting bacterial dispersal, which has implications for human health and the development of strategies aimed to redress the impact of westernization. © 2015 The Authors.
- Authors: Martínez, Inés , Stegen, James , Maldonado-Gómez, Maria , Eren, Murat , Siba, Peter , Greenhill, Andrew , Walter, Jens
- Date: 2015
- Type: Text , Journal article
- Relation: Cell Reports Vol. 11, no. 4 (2015), p. 527-538
- Full Text:
- Reviewed:
- Description: Although recent research revealed an impact of westernization on diversity and composition of the human gut microbiota, the exact consequences on metacommunity characteristics are insufficiently understood, and the underlying ecological mechanisms have not been elucidated. Here, we have compared the fecal microbiota of adults from two non-industrialized regions in Papua New Guinea (PNG) with that of United States (US) residents. Papua New Guineans harbor communities with greater bacterial diversity, lower inter-individual variation, vastly different abundance profiles, and bacterial lineages undetectable in US residents. A quantification of the ecological processes that govern community assembly identified bacterial dispersal as the dominant process that shapes the microbiome in PNG but not in the US. These findings suggest that the microbiome alterations detected in industrialized societies might arise from modern lifestyle factors limiting bacterial dispersal, which has implications for human health and the development of strategies aimed to redress the impact of westernization. © 2015 The Authors.
Childhood pneumonia and meningitis in the Eastern Highlands Province, Papua New Guinea in the era of conjugate vaccines: study methods and challenges
- Blyth, Christopher, Ford, Rebecca, Sapura, Joycelyn, Kumani, Tonny, Masiria, Geraldine, Kave, John, Yuasi, Lapule, Greenhill, Andrew, Hwaihwanje, Ilomo, Lang, Amanda, Lehmann, Deborah, Pomat, William
- Authors: Blyth, Christopher , Ford, Rebecca , Sapura, Joycelyn , Kumani, Tonny , Masiria, Geraldine , Kave, John , Yuasi, Lapule , Greenhill, Andrew , Hwaihwanje, Ilomo , Lang, Amanda , Lehmann, Deborah , Pomat, William
- Date: 2017
- Type: Text , Journal article
- Relation: Pneumonia Vol. 9, no. 1 (2017/03/05 2017), p. 5
- Full Text:
- Reviewed:
- Description: Background: Pneumonia and meningitis are common causes of severe childhood illness in Papua New Guinea (PNG). The etiology of both clinical conditions in PNG has not been recently assessed. Changes in lifestyle, provision and access to healthcare, antimicrobial utilization and resistance, and the national childhood vaccination schedule necessitate reassessment. Methods: A prospective case-control study was undertaken, enrolling children <5 years of age to determine the contemporary etiology of clinically defined moderate or severe pneumonia or suspected meningitis. Cases were identified following presentation for inpatient or outpatient care in Goroka town, the major population centre in the Eastern Highlands Province. Following enrolment, routine diagnostic specimens including blood, nasopharyngeal swabs, urine and (if required) cerebrospinal fluid, were obtained. Cases residing within one hour’s drive of Goroka were followed up, and recruitment of healthy contemporaneous controls was undertaken in the cases’ communities. Results: 998 cases and 978 controls were enrolled over 3 years. This included 784 cases (78.6%) with moderate pneumonia, 187 (18.7%) with severe pneumonia and 75 (7.5%) with suspected meningitis, of whom 48 (4.8%) had concurrent pneumonia. The median age of cases was 7.8 months (Interquartile range [IQR] 3.9–14.3), significantly lower than community controls, which was 20.8 months (IQR 8.2–36.4). Half the cases were admitted to hospital (500/998; 50.1%). Recruitment of cases and controls and successful collection of diagnostic specimens improved throughout the study, with blood volume increasing and rates of blood culture contamination decreasing. The overall case fatality rate was 18/998 (1.8%). Of cases eligible for follow-up, outcome data was available from 76.7%. Low but increasing coverage of Haemophilus influenzae type B conjugate vaccines on the national schedule was observed during the study period: three dose DTPw-HepB-Hib coverage in children >3 months increased from 14.9 to 43.0% and 29.0 to 47.7% in cases and controls (both p < 0.001). Despite inclusion in the national immunization program in 2014, 2015 PCV13 three-dose coverage in cases and controls >3 months was only 4.0 and 6.5%. Conclusions: Recruitment of large numbers of pediatric pneumonia and meningitis cases and community controls in a third-world setting presents unique challenges. Successful enrolment of 998 cases and 978 controls with comprehensive clinical data, biological specimens and follow up was achieved. Increased vaccine coverage remains an ongoing health priority.
- Authors: Blyth, Christopher , Ford, Rebecca , Sapura, Joycelyn , Kumani, Tonny , Masiria, Geraldine , Kave, John , Yuasi, Lapule , Greenhill, Andrew , Hwaihwanje, Ilomo , Lang, Amanda , Lehmann, Deborah , Pomat, William
- Date: 2017
- Type: Text , Journal article
- Relation: Pneumonia Vol. 9, no. 1 (2017/03/05 2017), p. 5
- Full Text:
- Reviewed:
- Description: Background: Pneumonia and meningitis are common causes of severe childhood illness in Papua New Guinea (PNG). The etiology of both clinical conditions in PNG has not been recently assessed. Changes in lifestyle, provision and access to healthcare, antimicrobial utilization and resistance, and the national childhood vaccination schedule necessitate reassessment. Methods: A prospective case-control study was undertaken, enrolling children <5 years of age to determine the contemporary etiology of clinically defined moderate or severe pneumonia or suspected meningitis. Cases were identified following presentation for inpatient or outpatient care in Goroka town, the major population centre in the Eastern Highlands Province. Following enrolment, routine diagnostic specimens including blood, nasopharyngeal swabs, urine and (if required) cerebrospinal fluid, were obtained. Cases residing within one hour’s drive of Goroka were followed up, and recruitment of healthy contemporaneous controls was undertaken in the cases’ communities. Results: 998 cases and 978 controls were enrolled over 3 years. This included 784 cases (78.6%) with moderate pneumonia, 187 (18.7%) with severe pneumonia and 75 (7.5%) with suspected meningitis, of whom 48 (4.8%) had concurrent pneumonia. The median age of cases was 7.8 months (Interquartile range [IQR] 3.9–14.3), significantly lower than community controls, which was 20.8 months (IQR 8.2–36.4). Half the cases were admitted to hospital (500/998; 50.1%). Recruitment of cases and controls and successful collection of diagnostic specimens improved throughout the study, with blood volume increasing and rates of blood culture contamination decreasing. The overall case fatality rate was 18/998 (1.8%). Of cases eligible for follow-up, outcome data was available from 76.7%. Low but increasing coverage of Haemophilus influenzae type B conjugate vaccines on the national schedule was observed during the study period: three dose DTPw-HepB-Hib coverage in children >3 months increased from 14.9 to 43.0% and 29.0 to 47.7% in cases and controls (both p < 0.001). Despite inclusion in the national immunization program in 2014, 2015 PCV13 three-dose coverage in cases and controls >3 months was only 4.0 and 6.5%. Conclusions: Recruitment of large numbers of pediatric pneumonia and meningitis cases and community controls in a third-world setting presents unique challenges. Successful enrolment of 998 cases and 978 controls with comprehensive clinical data, biological specimens and follow up was achieved. Increased vaccine coverage remains an ongoing health priority.
Clonal origins of Vibrio cholerae O1 El Tor strains, Papua New Guinea, 2009-2011
- Horwood, Paul, Collins, Deirdre, Jonduo, Marinjho, Rosewell, Alexander, Dutta, Samir, Dagina, Rosheila, Ropa, Berry, Siba, Peter, Greenhill, Andrew
- Authors: Horwood, Paul , Collins, Deirdre , Jonduo, Marinjho , Rosewell, Alexander , Dutta, Samir , Dagina, Rosheila , Ropa, Berry , Siba, Peter , Greenhill, Andrew
- Date: 2011
- Type: Text , Journal article
- Relation: Emerging Infectious Diseases Vol. 17, no. 11 (2011), p. 2063-2065
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- Description: We used multilocus sequence typing and variable number tandem repeat analysis to determine the clonal origins of Vibrio cholerae O1 El Tor strains from an outbreak of cholera that began in 2009 in Papua New Guinea. The epidemic is ongoing, and transmission risk is elevated within the Pacific region.
- Authors: Horwood, Paul , Collins, Deirdre , Jonduo, Marinjho , Rosewell, Alexander , Dutta, Samir , Dagina, Rosheila , Ropa, Berry , Siba, Peter , Greenhill, Andrew
- Date: 2011
- Type: Text , Journal article
- Relation: Emerging Infectious Diseases Vol. 17, no. 11 (2011), p. 2063-2065
- Full Text:
- Reviewed:
- Description: We used multilocus sequence typing and variable number tandem repeat analysis to determine the clonal origins of Vibrio cholerae O1 El Tor strains from an outbreak of cholera that began in 2009 in Papua New Guinea. The epidemic is ongoing, and transmission risk is elevated within the Pacific region.
Rationale and methods of a randomized controlled trial of immunogenicity, safety and impact on carriage of pneumococcal conjugate and polysaccharide vaccines in infants in Papua New Guinea
- Lehmann, Deborah, Kirarock, Wendy, van den Biggelaar, Anita, Passey, Megan, Jacoby, Peter, Saleu, Gerard, Masiria, Geraldine, Nivio, Birunu, Greenhill, Andrew, Orami, Tilda, Francis, Jacinta, Ford, Rebecca, Kirkham, Lea-Ann, Solomon, Vela, Richmond, Peter, Pomat, William
- Authors: Lehmann, Deborah , Kirarock, Wendy , van den Biggelaar, Anita , Passey, Megan , Jacoby, Peter , Saleu, Gerard , Masiria, Geraldine , Nivio, Birunu , Greenhill, Andrew , Orami, Tilda , Francis, Jacinta , Ford, Rebecca , Kirkham, Lea-Ann , Solomon, Vela , Richmond, Peter , Pomat, William
- Date: 2017
- Type: Text , Journal article
- Relation: Pneumonia Vol. 9, no. 20 (2017), p.
- Full Text:
- Reviewed:
- Description: Background: Children in third-world settings including Papua New Guinea (PNG) experience early onset of carriage with a broad range of pneumococcal serotypes, resulting in a high incidence of severe pneumococcal disease and deaths in the first 2 years of life. Vaccination trials in high endemicity settings are needed to provide evidence and guidance on optimal strategies to protect children in these settings against pneumococcal infections. Methods: This report describes the rationale, objectives, methods, study population, follow-up and specimen collection for a vaccination trial conducted in an endemic and logistically challenging setting in PNG. The trial aimed to determine whether currently available pneumococcal conjugate vaccines (PCV) are suitable for use under PNG’s accelerated immunization schedule, and that a schedule including pneumococcal polysaccharide vaccine (PPV) in later infancy is safe and immunogenic in this high-risk population. Results: This open randomized-controlled trial was conducted between November 2011 and March 2016, enrolling 262 children aged 1 month between November 2011 and April 2014. The participants were randomly allocated (1:1) to receive 10-valent PCV (10vPCV) or 13-valent PCV (13vPCV) in a 1-2-3-month schedule, with further randomization to receive PPV or no PPV at age 9 months, followed by a 1/5th PPV challenge at age 23 months. A total of 1229 blood samples were collected to measure humoral and cellular immune responses and 1238 nasopharyngeal swabs to assess upper respiratory tract colonization and carriage load. Serious adverse events were monitored throughout the study. Of the 262 children enrolled, 87% received 3 doses of PCV, 79% were randomized to receive PPV or no PPV at age 9 months, and 67% completed the study at 24 months of age with appropriate immunization and challenge. Conclusion: Laboratory testing of the many samples collected during this trial will determine the impact of the different vaccine schedules and formulations on nasopharyngeal carriage, antibody production and function, and immune memory. The final data will inform policy on pneumococcal vaccine schedules in countries with children at high risk of pneumococcal disease by providing direct comparison of an accelerated schedule of 10vPCV and 13vPCV and the potential advantages of PPV following PCV immunization
- Authors: Lehmann, Deborah , Kirarock, Wendy , van den Biggelaar, Anita , Passey, Megan , Jacoby, Peter , Saleu, Gerard , Masiria, Geraldine , Nivio, Birunu , Greenhill, Andrew , Orami, Tilda , Francis, Jacinta , Ford, Rebecca , Kirkham, Lea-Ann , Solomon, Vela , Richmond, Peter , Pomat, William
- Date: 2017
- Type: Text , Journal article
- Relation: Pneumonia Vol. 9, no. 20 (2017), p.
- Full Text:
- Reviewed:
- Description: Background: Children in third-world settings including Papua New Guinea (PNG) experience early onset of carriage with a broad range of pneumococcal serotypes, resulting in a high incidence of severe pneumococcal disease and deaths in the first 2 years of life. Vaccination trials in high endemicity settings are needed to provide evidence and guidance on optimal strategies to protect children in these settings against pneumococcal infections. Methods: This report describes the rationale, objectives, methods, study population, follow-up and specimen collection for a vaccination trial conducted in an endemic and logistically challenging setting in PNG. The trial aimed to determine whether currently available pneumococcal conjugate vaccines (PCV) are suitable for use under PNG’s accelerated immunization schedule, and that a schedule including pneumococcal polysaccharide vaccine (PPV) in later infancy is safe and immunogenic in this high-risk population. Results: This open randomized-controlled trial was conducted between November 2011 and March 2016, enrolling 262 children aged 1 month between November 2011 and April 2014. The participants were randomly allocated (1:1) to receive 10-valent PCV (10vPCV) or 13-valent PCV (13vPCV) in a 1-2-3-month schedule, with further randomization to receive PPV or no PPV at age 9 months, followed by a 1/5th PPV challenge at age 23 months. A total of 1229 blood samples were collected to measure humoral and cellular immune responses and 1238 nasopharyngeal swabs to assess upper respiratory tract colonization and carriage load. Serious adverse events were monitored throughout the study. Of the 262 children enrolled, 87% received 3 doses of PCV, 79% were randomized to receive PPV or no PPV at age 9 months, and 67% completed the study at 24 months of age with appropriate immunization and challenge. Conclusion: Laboratory testing of the many samples collected during this trial will determine the impact of the different vaccine schedules and formulations on nasopharyngeal carriage, antibody production and function, and immune memory. The final data will inform policy on pneumococcal vaccine schedules in countries with children at high risk of pneumococcal disease by providing direct comparison of an accelerated schedule of 10vPCV and 13vPCV and the potential advantages of PPV following PCV immunization
The PneuCarriage Project : A multi-centre comparative study to identify the best serotyping methods for examining pneumococcal carriage in vaccine evaluation studies
- Satzke, Catherine, Dunne, Eileen, Porter, Barbara, Klugman, Keith, Mulholland, Kim, PneuCarriage project group, Greenhill, Andrew
- Authors: Satzke, Catherine , Dunne, Eileen , Porter, Barbara , Klugman, Keith , Mulholland, Kim , PneuCarriage project group , Greenhill, Andrew
- Date: 2015
- Type: Text , Journal article
- Relation: PLoS Medicine Vol. 12, no. 11 (2015), p. 1-30
- Full Text:
- Reviewed:
- Description: Background: The pneumococcus is a diverse pathogen whose primary niche is the nasopharynx. Over 90 different serotypes exist, and nasopharyngeal carriage of multiple serotypes is common. Understanding pneumococcal carriage is essential for evaluating the impact of pneumococcal vaccines. Traditional serotyping methods are cumbersome and insufficient for detecting multiple serotype carriage, and there are few data comparing the new methods that have been developed over the past decade. We established the PneuCarriage project, a large, international multi-centre study dedicated to the identification of the best pneumococcal serotyping methods for carriage studies. Methods and Findings: Reference sample sets were distributed to 15 research groups for blinded testing. Twenty pneumococcal serotyping methods were used to test 81 laboratory-prepared (spiked) samples. The five top-performing methods were used to test 260 nasopharyngeal (field) samples collected from children in six high-burden countries. Sensitivity and positive predictive value (PPV) were determined for the test methods and the reference method (traditional serotyping of >100 colonies from each sample). For the alternate serotyping methods, the overall sensitivity ranged from 1% to 99% (reference method 98%), and PPV from 8% to 100% (reference method 100%), when testing the spiked samples. Fifteen methods had ≥70% sensitivity to detect the dominant (major) serotype, whilst only eight methods had ≥70% sensitivity to detect minor serotypes. For the field samples, the overall sensitivity ranged from 74.2% to 95.8% (reference method 93.8%), and PPV from 82.2% to 96.4% (reference method 99.6%). The microarray had the highest sensitivity (95.8%) and high PPV (93.7%). The major limitation of this study is that not all of the available alternative serotyping methods were included. Conclusions: Most methods were able to detect the dominant serotype in a sample, but many performed poorly in detecting the minor serotype populations. Microarray with a culture amplification step was the top-performing method. Results from this comprehensive evaluation will inform future vaccine evaluation and impact studies, particularly in low-income settings, where pneumococcal disease burden remains high. © 2015 Satzke et al. *For a complete list of authors, please see acknowledgments in the published article.
- Authors: Satzke, Catherine , Dunne, Eileen , Porter, Barbara , Klugman, Keith , Mulholland, Kim , PneuCarriage project group , Greenhill, Andrew
- Date: 2015
- Type: Text , Journal article
- Relation: PLoS Medicine Vol. 12, no. 11 (2015), p. 1-30
- Full Text:
- Reviewed:
- Description: Background: The pneumococcus is a diverse pathogen whose primary niche is the nasopharynx. Over 90 different serotypes exist, and nasopharyngeal carriage of multiple serotypes is common. Understanding pneumococcal carriage is essential for evaluating the impact of pneumococcal vaccines. Traditional serotyping methods are cumbersome and insufficient for detecting multiple serotype carriage, and there are few data comparing the new methods that have been developed over the past decade. We established the PneuCarriage project, a large, international multi-centre study dedicated to the identification of the best pneumococcal serotyping methods for carriage studies. Methods and Findings: Reference sample sets were distributed to 15 research groups for blinded testing. Twenty pneumococcal serotyping methods were used to test 81 laboratory-prepared (spiked) samples. The five top-performing methods were used to test 260 nasopharyngeal (field) samples collected from children in six high-burden countries. Sensitivity and positive predictive value (PPV) were determined for the test methods and the reference method (traditional serotyping of >100 colonies from each sample). For the alternate serotyping methods, the overall sensitivity ranged from 1% to 99% (reference method 98%), and PPV from 8% to 100% (reference method 100%), when testing the spiked samples. Fifteen methods had ≥70% sensitivity to detect the dominant (major) serotype, whilst only eight methods had ≥70% sensitivity to detect minor serotypes. For the field samples, the overall sensitivity ranged from 74.2% to 95.8% (reference method 93.8%), and PPV from 82.2% to 96.4% (reference method 99.6%). The microarray had the highest sensitivity (95.8%) and high PPV (93.7%). The major limitation of this study is that not all of the available alternative serotyping methods were included. Conclusions: Most methods were able to detect the dominant serotype in a sample, but many performed poorly in detecting the minor serotype populations. Microarray with a culture amplification step was the top-performing method. Results from this comprehensive evaluation will inform future vaccine evaluation and impact studies, particularly in low-income settings, where pneumococcal disease burden remains high. © 2015 Satzke et al. *For a complete list of authors, please see acknowledgments in the published article.
Influenza A(H5N1) viruses with A(H9N2) single gene (matrix or PB1) reassortment isolated from Cambodian live bird markets
- Suttie, Annika, Karlsson, Erik, Deng, Yi-Mo, Horm, Srey, Yann, Sokhoun, Tok, Songha, Sorn, San, Holl, Davun, Tum, Sothyra, Hurt, Aeron, Greenhill, Andrew, Barr, Ian, Horwood, Paul, Dussart, Philippe
- Authors: Suttie, Annika , Karlsson, Erik , Deng, Yi-Mo , Horm, Srey , Yann, Sokhoun , Tok, Songha , Sorn, San , Holl, Davun , Tum, Sothyra , Hurt, Aeron , Greenhill, Andrew , Barr, Ian , Horwood, Paul , Dussart, Philippe
- Date: 2018
- Type: Text , Journal article
- Relation: Virology Vol. 523, no. (2018), p. 22-26
- Full Text:
- Reviewed:
- Description: Live bird market surveillance for avian influenza viruses in Cambodia in 2015 has led to the detection of two 7:1 reassortant influenza A(H5N1) clade 2.3.2.1c viruses. These reassortant strains, designated A/duck/Cambodia/Z564W35M1/2015 and A/chicken/Cambodia/Z850W49M1/2015, both contained a single gene (PB1 and matrix gene, respectively) from concurrently circulating A(H9N2) influenza viruses. All other viral genes from both isolates clustered with A(H5N1) clade 2.3.2.1 viruses. Continued and prolonged co-circulation of influenza A(H5N1) and A(H9N2) viruses in Cambodian live bird markets may present a risk for the emergence of novel influenza reassortant viruses with negative agricultural and/or public health implications. © 2018
- Authors: Suttie, Annika , Karlsson, Erik , Deng, Yi-Mo , Horm, Srey , Yann, Sokhoun , Tok, Songha , Sorn, San , Holl, Davun , Tum, Sothyra , Hurt, Aeron , Greenhill, Andrew , Barr, Ian , Horwood, Paul , Dussart, Philippe
- Date: 2018
- Type: Text , Journal article
- Relation: Virology Vol. 523, no. (2018), p. 22-26
- Full Text:
- Reviewed:
- Description: Live bird market surveillance for avian influenza viruses in Cambodia in 2015 has led to the detection of two 7:1 reassortant influenza A(H5N1) clade 2.3.2.1c viruses. These reassortant strains, designated A/duck/Cambodia/Z564W35M1/2015 and A/chicken/Cambodia/Z850W49M1/2015, both contained a single gene (PB1 and matrix gene, respectively) from concurrently circulating A(H9N2) influenza viruses. All other viral genes from both isolates clustered with A(H5N1) clade 2.3.2.1 viruses. Continued and prolonged co-circulation of influenza A(H5N1) and A(H9N2) viruses in Cambodian live bird markets may present a risk for the emergence of novel influenza reassortant viruses with negative agricultural and/or public health implications. © 2018
Detection of enteric viral and bacterial pathogens associated with paediatric diarrhoea in Goroka, Papua New Guinea
- Soli, Kevin, Maure, Tobias, Kas, Monalisa, Bande, Grace, Bebes, Sauli, Luang-Suarkia, Dagwin, Siba, Peter, Morita, Ayako, Umezaki, Masahiro, Greenhill, Andrew, Horwood, Paul
- Authors: Soli, Kevin , Maure, Tobias , Kas, Monalisa , Bande, Grace , Bebes, Sauli , Luang-Suarkia, Dagwin , Siba, Peter , Morita, Ayako , Umezaki, Masahiro , Greenhill, Andrew , Horwood, Paul
- Date: 2014
- Type: Text , Journal article
- Relation: International Journal of Infectious Diseases Vol. 27, no. (2014), p. 54-58
- Full Text:
- Reviewed:
- Description: Objectives: The aim of this study was to investigate the viral and bacterial causes of acute watery diarrhoea in hospitalized children in Papua New Guinea. Methods: A retrospective analysis was conducted on stool samples collected from 199 children (age > 5 years) admitted to the paediatric ward of Goroka General Hospital from August 2009 through November 2010. A large range of viral and bacterial enteric pathogens were targeted using real-time PCR/RT-PCR assays. Results: Young children were much more likely to be admitted with acute gastroenteritis, with 62.8% of patients aged >1 year and 88.4% aged >2 years. An enteric pathogen was detected in 69.8% (n= 138) of patients. The most commonly detected pathogens were Shigella spp (26.6%), rotavirus (25.6%), adenovirus types 40/41 (11.6%), enterotoxigenic Escherichia coli (11.1%), enteropathogenic E. coli (8.5%), norovirus G2 (6.0%), and Campylobacter spp (4.0%). Norovirus G1, sapovirus, and Salmonella spp were also detected, but below our statistical limit of detection. Vibrio cholerae and astrovirus were not detected in any patients. Mixed infections were detected in 22.1% of patients, with Shigella and rotavirus most commonly detected in co-infections with other pathogens. Conclusions: This study demonstrates that Shigella and rotavirus are the major pathogens associated with acute paediatric gastroenteritis in this setting. © 2014 The Authors.
- Authors: Soli, Kevin , Maure, Tobias , Kas, Monalisa , Bande, Grace , Bebes, Sauli , Luang-Suarkia, Dagwin , Siba, Peter , Morita, Ayako , Umezaki, Masahiro , Greenhill, Andrew , Horwood, Paul
- Date: 2014
- Type: Text , Journal article
- Relation: International Journal of Infectious Diseases Vol. 27, no. (2014), p. 54-58
- Full Text:
- Reviewed:
- Description: Objectives: The aim of this study was to investigate the viral and bacterial causes of acute watery diarrhoea in hospitalized children in Papua New Guinea. Methods: A retrospective analysis was conducted on stool samples collected from 199 children (age > 5 years) admitted to the paediatric ward of Goroka General Hospital from August 2009 through November 2010. A large range of viral and bacterial enteric pathogens were targeted using real-time PCR/RT-PCR assays. Results: Young children were much more likely to be admitted with acute gastroenteritis, with 62.8% of patients aged >1 year and 88.4% aged >2 years. An enteric pathogen was detected in 69.8% (n= 138) of patients. The most commonly detected pathogens were Shigella spp (26.6%), rotavirus (25.6%), adenovirus types 40/41 (11.6%), enterotoxigenic Escherichia coli (11.1%), enteropathogenic E. coli (8.5%), norovirus G2 (6.0%), and Campylobacter spp (4.0%). Norovirus G1, sapovirus, and Salmonella spp were also detected, but below our statistical limit of detection. Vibrio cholerae and astrovirus were not detected in any patients. Mixed infections were detected in 22.1% of patients, with Shigella and rotavirus most commonly detected in co-infections with other pathogens. Conclusions: This study demonstrates that Shigella and rotavirus are the major pathogens associated with acute paediatric gastroenteritis in this setting. © 2014 The Authors.
Spatio-temporal epidemiology of the cholera outbreak in Papua New Guinea, 2009-2011
- Horwood, Paul, Karl, Stephan, Mueller, Ivo, Jonduo, Marinjho, Pavlin, Boris, Dagina, Rosheila, Ropa, Berry, Bieb, Sibauk, Rosewell, Alexander, Umezaki, Masahiro, Siba, Peter, Greenhill, Andrew
- Authors: Horwood, Paul , Karl, Stephan , Mueller, Ivo , Jonduo, Marinjho , Pavlin, Boris , Dagina, Rosheila , Ropa, Berry , Bieb, Sibauk , Rosewell, Alexander , Umezaki, Masahiro , Siba, Peter , Greenhill, Andrew
- Date: 2014
- Type: Text , Journal article
- Relation: BMC Infectious Diseases Vol. 14, no. 1 (2014), p.
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- Description: Background: Cholera continues to be a devastating disease in many developing countries where inadequate safe water supply and poor sanitation facilitate spread. From July 2009 until late 2011 Papua New Guinea experienced the first outbreak of cholera recorded in the country, resulting in > 15,500 cases and > 500 deaths. Methods: Using the national cholera database, we analysed the spatio-temporal distribution and clustering of the Papua New Guinea cholera outbreak. The Kulldorff space-time permutation scan statistic, contained in the software package SatScan v9.2 was used to describe the first 8 weeks of the outbreak in Morobe Province before cholera cases spread throughout other regions of the country. Data were aggregated at the provincial level to describe the spread of the disease to other affected provinces. Results: Spatio-temporal and cluster analyses revealed that the outbreak was characterized by three distinct phases punctuated by explosive propagation of cases when the outbreak spread to a new region. The lack of road networks across most of Papua New Guinea is likely to have had a major influence on the slow spread of the disease during this outbreak. Conclusions: Identification of high risk areas and the likely mode of spread can guide government health authorities to formulate public health strategies to mitigate the spread of the disease through education campaigns, vaccination, increased surveillance in targeted areas and interventions to improve water, sanitation and hygiene.
- Authors: Horwood, Paul , Karl, Stephan , Mueller, Ivo , Jonduo, Marinjho , Pavlin, Boris , Dagina, Rosheila , Ropa, Berry , Bieb, Sibauk , Rosewell, Alexander , Umezaki, Masahiro , Siba, Peter , Greenhill, Andrew
- Date: 2014
- Type: Text , Journal article
- Relation: BMC Infectious Diseases Vol. 14, no. 1 (2014), p.
- Full Text:
- Reviewed:
- Description: Background: Cholera continues to be a devastating disease in many developing countries where inadequate safe water supply and poor sanitation facilitate spread. From July 2009 until late 2011 Papua New Guinea experienced the first outbreak of cholera recorded in the country, resulting in > 15,500 cases and > 500 deaths. Methods: Using the national cholera database, we analysed the spatio-temporal distribution and clustering of the Papua New Guinea cholera outbreak. The Kulldorff space-time permutation scan statistic, contained in the software package SatScan v9.2 was used to describe the first 8 weeks of the outbreak in Morobe Province before cholera cases spread throughout other regions of the country. Data were aggregated at the provincial level to describe the spread of the disease to other affected provinces. Results: Spatio-temporal and cluster analyses revealed that the outbreak was characterized by three distinct phases punctuated by explosive propagation of cases when the outbreak spread to a new region. The lack of road networks across most of Papua New Guinea is likely to have had a major influence on the slow spread of the disease during this outbreak. Conclusions: Identification of high risk areas and the likely mode of spread can guide government health authorities to formulate public health strategies to mitigate the spread of the disease through education campaigns, vaccination, increased surveillance in targeted areas and interventions to improve water, sanitation and hygiene.
Respiratory viral pathogens associated with lower respiratory tract disease among young children in the highlands of Papua New Guinea
- Chidlow, Glenys, Laing, Ingrid, Harnett, Gerald, Greenhill, Andrew, Phuanukoonnon, Suparat, Siba, Peter, Pomat, William, Shellam, Geoffrey, Smith, David, Lehmann, Deborah
- Authors: Chidlow, Glenys , Laing, Ingrid , Harnett, Gerald , Greenhill, Andrew , Phuanukoonnon, Suparat , Siba, Peter , Pomat, William , Shellam, Geoffrey , Smith, David , Lehmann, Deborah
- Date: 2012
- Type: Text , Journal article
- Relation: Journal of Clinical Virology Vol. 54, no. 3 (2012), p. 235-239
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- Description: Background: Acute lower respiratory tract infections (ALRI) commonly result in fatal outcomes in the young children of Papua New Guinea (PNG). However, comprehensive studies of the viral aetiology of ALRI have not been conducted in PNG for almost 30 years. Objectives: To determine the viruses associated with ALRI among children living in the PNG highlands using sensitive molecular detection techniques. Study design: Pernasal swabs were collected routinely between 1 week and 18 months of age and also during episodes of ALRI, as part of a neonatal pneumococcal conjugate vaccine trial. A tandem multiplex real-time PCR assay was used to test for a comprehensive range of respiratory viruses in samples collected from 221 young children. Picornavirus typing was supported by DNA sequence analysis. Results: Recognized pathogenic respiratory viruses were detected in 198/273 (73%) samples collected from children with no evidence of ALRI and 69/80 (86%) samples collected during ALRI episodes. Human rhinoviruses (HRV) species A, B and C were detected in 152 (56%) samples from non-ALRI children and 50 (63%) samples collected during ALRI episodes. Partial structural region sequences for two new species C rhinoviruses were added to the GenBank database. ALRI was associated with detection of adenovirus species B (p< 0.01) or C (p< 0.05), influenza A (p< 0.0001) or respiratory syncytial virus (p< 0.0001). Multiple viruses were detected more often during ALRI episodes (49%) than when children displayed no symptoms of ALRI (18%) (p< 0.0001). Conclusions: The burden of infection with respiratory viruses remains significant in young children living in the PNG highlands.
- Authors: Chidlow, Glenys , Laing, Ingrid , Harnett, Gerald , Greenhill, Andrew , Phuanukoonnon, Suparat , Siba, Peter , Pomat, William , Shellam, Geoffrey , Smith, David , Lehmann, Deborah
- Date: 2012
- Type: Text , Journal article
- Relation: Journal of Clinical Virology Vol. 54, no. 3 (2012), p. 235-239
- Full Text:
- Reviewed:
- Description: Background: Acute lower respiratory tract infections (ALRI) commonly result in fatal outcomes in the young children of Papua New Guinea (PNG). However, comprehensive studies of the viral aetiology of ALRI have not been conducted in PNG for almost 30 years. Objectives: To determine the viruses associated with ALRI among children living in the PNG highlands using sensitive molecular detection techniques. Study design: Pernasal swabs were collected routinely between 1 week and 18 months of age and also during episodes of ALRI, as part of a neonatal pneumococcal conjugate vaccine trial. A tandem multiplex real-time PCR assay was used to test for a comprehensive range of respiratory viruses in samples collected from 221 young children. Picornavirus typing was supported by DNA sequence analysis. Results: Recognized pathogenic respiratory viruses were detected in 198/273 (73%) samples collected from children with no evidence of ALRI and 69/80 (86%) samples collected during ALRI episodes. Human rhinoviruses (HRV) species A, B and C were detected in 152 (56%) samples from non-ALRI children and 50 (63%) samples collected during ALRI episodes. Partial structural region sequences for two new species C rhinoviruses were added to the GenBank database. ALRI was associated with detection of adenovirus species B (p< 0.01) or C (p< 0.05), influenza A (p< 0.0001) or respiratory syncytial virus (p< 0.0001). Multiple viruses were detected more often during ALRI episodes (49%) than when children displayed no symptoms of ALRI (18%) (p< 0.0001). Conclusions: The burden of infection with respiratory viruses remains significant in young children living in the PNG highlands.
A large outbreak of shigellosis commencing in an internally displaced population, Papua New Guinea, 2013
- Benny, Edwin, Mesere, Kelly, Pavlin, Boris, Yakam, Logan, Ford, Rebecca, Yoannes, Mition, Kisa, Debbie, Abdad, Mohammad, Menda, Lincoln, Greenhill, Andrew, Horwood, Paul
- Authors: Benny, Edwin , Mesere, Kelly , Pavlin, Boris , Yakam, Logan , Ford, Rebecca , Yoannes, Mition , Kisa, Debbie , Abdad, Mohammad , Menda, Lincoln , Greenhill, Andrew , Horwood, Paul
- Date: 2014
- Type: Text , Journal article
- Relation: Western Pacific surveillance and response journal : WPSAR Vol. 5, no. 3 (2014), p. 18-21
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- Description: OBJECTIVE: The objective of this study was to investigate a large outbreak of shigellosis in Papua New Guinea that began in a camp for internally displaced persons before spreading throughout the general community. METHODS: Outbreak mitigation strategies were implemented in the affected area to curtail the spread of the disease. Data were collected from the surveillance system and analysed by time, place and person. Rectal swab samples were tested by standard culture methods and real-time polymerase chain reaction to determine the etiology of the outbreak. RESULTS: Laboratory analysis at two independent institutions established that the outbreak was caused by Shigella sp., with one strain further characterized as Shigella flexneri serotype 2. Approximately 1200 suspected cases of shigellosis were reported in a two-month period from two townships in Morobe Province, Papua New Guinea. The outbreak resulted in at least five deaths, all in young children. DISCUSSION: This outbreak of shigellosis highlights the threat of enteric diseases to vulnerable populations such as internally displaced persons in Papua New Guinea, as has been observed in other global settings.
- Authors: Benny, Edwin , Mesere, Kelly , Pavlin, Boris , Yakam, Logan , Ford, Rebecca , Yoannes, Mition , Kisa, Debbie , Abdad, Mohammad , Menda, Lincoln , Greenhill, Andrew , Horwood, Paul
- Date: 2014
- Type: Text , Journal article
- Relation: Western Pacific surveillance and response journal : WPSAR Vol. 5, no. 3 (2014), p. 18-21
- Full Text:
- Reviewed:
- Description: OBJECTIVE: The objective of this study was to investigate a large outbreak of shigellosis in Papua New Guinea that began in a camp for internally displaced persons before spreading throughout the general community. METHODS: Outbreak mitigation strategies were implemented in the affected area to curtail the spread of the disease. Data were collected from the surveillance system and analysed by time, place and person. Rectal swab samples were tested by standard culture methods and real-time polymerase chain reaction to determine the etiology of the outbreak. RESULTS: Laboratory analysis at two independent institutions established that the outbreak was caused by Shigella sp., with one strain further characterized as Shigella flexneri serotype 2. Approximately 1200 suspected cases of shigellosis were reported in a two-month period from two townships in Morobe Province, Papua New Guinea. The outbreak resulted in at least five deaths, all in young children. DISCUSSION: This outbreak of shigellosis highlights the threat of enteric diseases to vulnerable populations such as internally displaced persons in Papua New Guinea, as has been observed in other global settings.
Health challenges of the pacific region : Insights from history, geography, social determinants, genetics, and the microbiome
- Horwood, Paul, Tarantola, Arnaud, Goarant, Cyrille, Matsui, Mariko, Klement, Elise, Umezaki, Masahiro, Navarro, Severine, Greenhill, Andrew
- Authors: Horwood, Paul , Tarantola, Arnaud , Goarant, Cyrille , Matsui, Mariko , Klement, Elise , Umezaki, Masahiro , Navarro, Severine , Greenhill, Andrew
- Date: 2019
- Type: Text , Journal article , Review
- Relation: Frontiers in Immunology Vol. 10, no. (2019), p. 1-16
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- Description: The Pacific region, also referred to as Oceania, is a geographically widespread region populated by people of diverse cultures and ethnicities. Indigenous people in the region (Melanesians, Polynesians, Micronesians, Papuans, and Indigenous Australians) are over-represented on national, regional, and global scales for the burden of infectious and non-communicable diseases. Although social and environmental factors such as poverty, education, and access to health-care are assumed to be major drivers of this disease burden, there is also developing evidence that genetic and microbiotic factors should also be considered. To date, studies investigating genetic and/or microbiotic links with vulnerabilities to infectious and non-communicable diseases have mostly focused on populations in Europe, Asia, and USA, with uncertain associations for other populations such as indigenous communities in Oceania. Recent developments in personalized medicine have shown that identifying ethnicity-linked genetic vulnerabilities can be important for medical management. Although our understanding of the impacts of the gut microbiome on health is still in the early stages, it is likely that equivalent vulnerabilities will also be identified through the interaction between gut microbiome composition and function with pathogens and the host immune system. As rapid economic, dietary, and cultural changes occur throughout Oceania it becomes increasingly important that further research is conducted within indigenous populations to address the double burden of high rates of infectious diseases and rapidly rising non-communicable diseases so that comprehensive development goals can be planned. In this article, we review the current knowledge on the impact of nutrition, genetics, and the gut microbiome on infectious diseases in indigenous people of the Pacific region.
- Authors: Horwood, Paul , Tarantola, Arnaud , Goarant, Cyrille , Matsui, Mariko , Klement, Elise , Umezaki, Masahiro , Navarro, Severine , Greenhill, Andrew
- Date: 2019
- Type: Text , Journal article , Review
- Relation: Frontiers in Immunology Vol. 10, no. (2019), p. 1-16
- Full Text:
- Reviewed:
- Description: The Pacific region, also referred to as Oceania, is a geographically widespread region populated by people of diverse cultures and ethnicities. Indigenous people in the region (Melanesians, Polynesians, Micronesians, Papuans, and Indigenous Australians) are over-represented on national, regional, and global scales for the burden of infectious and non-communicable diseases. Although social and environmental factors such as poverty, education, and access to health-care are assumed to be major drivers of this disease burden, there is also developing evidence that genetic and microbiotic factors should also be considered. To date, studies investigating genetic and/or microbiotic links with vulnerabilities to infectious and non-communicable diseases have mostly focused on populations in Europe, Asia, and USA, with uncertain associations for other populations such as indigenous communities in Oceania. Recent developments in personalized medicine have shown that identifying ethnicity-linked genetic vulnerabilities can be important for medical management. Although our understanding of the impacts of the gut microbiome on health is still in the early stages, it is likely that equivalent vulnerabilities will also be identified through the interaction between gut microbiome composition and function with pathogens and the host immune system. As rapid economic, dietary, and cultural changes occur throughout Oceania it becomes increasingly important that further research is conducted within indigenous populations to address the double burden of high rates of infectious diseases and rapidly rising non-communicable diseases so that comprehensive development goals can be planned. In this article, we review the current knowledge on the impact of nutrition, genetics, and the gut microbiome on infectious diseases in indigenous people of the Pacific region.
Methicillin-resistant staphylococcus aureus in Melanesian children with haematogenous osteomyelitis from the Central Highlands of Papua New Guinea
- Aglua, Izzard, Jaworski, Jan, Drekore, Jimmy, Urakoko, Bohu, Poka, Harry, Michael, Audrey, Greenhill, Andrew
- Authors: Aglua, Izzard , Jaworski, Jan , Drekore, Jimmy , Urakoko, Bohu , Poka, Harry , Michael, Audrey , Greenhill, Andrew
- Date: 2018
- Type: Text , Journal article
- Relation: International Journal of Pediatrics Vol. 6, no. 10 (2018), p. 8361-8370
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- Description: Background: Methicillin-Resistant Staphylococcus aureus (MRSA) has been an important cause of bone infection since the 1940s. Current guidelines recommend targeted antibiotic use for osteomyelitis treatment informed by microbial sensitivity patterns. However, in settings without microbiology facilities, empirical antibiotic use is common. Unrecognized antibiotic resistance potentiates persistence of MRSA with osteomyelitis progression to chronic forms with complications despite antibiotic treatment. Materials and Methods: A prospective observational study was done to identify common etiological agent (s) in bone infection in Melanesian children (that were admitted to the two surgical and one pediatric wards of the SJNM-KUGH in the Simbu province of Papua New Guinea in 2012 and 2017), observe for presence of antimicrobial resistance, and determine effective antibiotic regimes for treatment of bone pediatric osteomyelitis. Seventy pediatric patients presenting from the community with osteomyelitis were recruited, with bone and non-bone specimens sampled, cultured and isolates tested for resistance to common antibiotics. Results: Staphylococcus aureus (S. aureus) was isolated in 67% (47/70) of collected specimens. Of the 47 isolates, there was 91.5% resistance to penicillin, 85.1% resistance to methicillin, 89.4% resistance to oxacillin, 93.6% resistance to ampicillin and 80.9% resistance to ceftriaxone. S. aureus showed 91.5% sensitivity to gentamycin, 93.6% sensitivity to erythromycin, tetracycline and clindamycin, and 95.7% sensitivity to Co-trimoxazole. Conclusion: MRSA was the leading cause of haematogenous osteomyelitis in Melanesian children. S.aureus was isolated mainly from infected long bones of the lower limbs (79%) of children presenting from the community, suggesting a predominantly community-associated MRSA.
- Authors: Aglua, Izzard , Jaworski, Jan , Drekore, Jimmy , Urakoko, Bohu , Poka, Harry , Michael, Audrey , Greenhill, Andrew
- Date: 2018
- Type: Text , Journal article
- Relation: International Journal of Pediatrics Vol. 6, no. 10 (2018), p. 8361-8370
- Full Text:
- Reviewed:
- Description: Background: Methicillin-Resistant Staphylococcus aureus (MRSA) has been an important cause of bone infection since the 1940s. Current guidelines recommend targeted antibiotic use for osteomyelitis treatment informed by microbial sensitivity patterns. However, in settings without microbiology facilities, empirical antibiotic use is common. Unrecognized antibiotic resistance potentiates persistence of MRSA with osteomyelitis progression to chronic forms with complications despite antibiotic treatment. Materials and Methods: A prospective observational study was done to identify common etiological agent (s) in bone infection in Melanesian children (that were admitted to the two surgical and one pediatric wards of the SJNM-KUGH in the Simbu province of Papua New Guinea in 2012 and 2017), observe for presence of antimicrobial resistance, and determine effective antibiotic regimes for treatment of bone pediatric osteomyelitis. Seventy pediatric patients presenting from the community with osteomyelitis were recruited, with bone and non-bone specimens sampled, cultured and isolates tested for resistance to common antibiotics. Results: Staphylococcus aureus (S. aureus) was isolated in 67% (47/70) of collected specimens. Of the 47 isolates, there was 91.5% resistance to penicillin, 85.1% resistance to methicillin, 89.4% resistance to oxacillin, 93.6% resistance to ampicillin and 80.9% resistance to ceftriaxone. S. aureus showed 91.5% sensitivity to gentamycin, 93.6% sensitivity to erythromycin, tetracycline and clindamycin, and 95.7% sensitivity to Co-trimoxazole. Conclusion: MRSA was the leading cause of haematogenous osteomyelitis in Melanesian children. S.aureus was isolated mainly from infected long bones of the lower limbs (79%) of children presenting from the community, suggesting a predominantly community-associated MRSA.
Antibiotic resistant Shigella is a major cause of diarrhoea in the Highlands of Papua New Guinea
- Greenhill, Andrew, Guwada, Carlton, Siba, Valentine, Michael, Audrey, Yoannes, Mution, Wawarie, Yolandah, Ford, Rebecca, Siba, Peter, Horwood, Paul
- Authors: Greenhill, Andrew , Guwada, Carlton , Siba, Valentine , Michael, Audrey , Yoannes, Mution , Wawarie, Yolandah , Ford, Rebecca , Siba, Peter , Horwood, Paul
- Date: 2014
- Type: Text , Journal article
- Relation: Journal of Infection in Developing Countries Vol. 8, no. 11 (2014), p. 1391-1397
- Full Text:
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- Description: Introduction: Diarrhoea remains a major cause of illness in Papua New Guinea (PNG); however, little is known about its aetiology. As a result of the cholera outbreak that spread throughout PNG in 2009-2011, we conducted diarrhoeal surveillance in Eastern Highlands Province. Methodology: Following informed consent and a brief questionnaire, participants provided a stool sample or duplicate rectal swabs. Samples were tested for common bacterial pathogens Salmonella spp., Shigella spp., Vibrio spp., Campylobacter spp. and Yersinia enterocolitica using established culture methods. Enteric parasites were detected using microscopy. Results: A total of 216 participants were enrolled; where age was recorded, 42% were under 5 years of age, 6.7% were 5 to 17 years of age and 51.3% ≥18 years of age. One or more pathogens were detected in 68 (31.5%) participants, with Shigella (primarily S. flexneri) being the most commonly isolated (47 of 216 participants). Enteric parasites were detected in 23 of the 216 participants, occurring as a co-infection with another pathogen in 12 of 23 cases. No Vibrio cholerae was detected. Shigella isolates were commonly resistant to ampicillin, tetracycline, co-trimoxazole and chloramphenicol. Conclusions: Shigellae, specifically S. flexneri, are important pathogens in the highlands of PNG. While most studies in low-income settings focus on childhood aetiology, we have demonstrated the importance of Shigella in both children and adults. Enteric parasites remain present and presumably contribute to the burden of gastrointestinal illness. While improvements in sanitation and hygiene would help lower the burden of all aetiologies of infectious diarrhoea, additional control strategies targeting Shigella may also be warranted. © 2014 Greenhill et al.
- Authors: Greenhill, Andrew , Guwada, Carlton , Siba, Valentine , Michael, Audrey , Yoannes, Mution , Wawarie, Yolandah , Ford, Rebecca , Siba, Peter , Horwood, Paul
- Date: 2014
- Type: Text , Journal article
- Relation: Journal of Infection in Developing Countries Vol. 8, no. 11 (2014), p. 1391-1397
- Full Text:
- Reviewed:
- Description: Introduction: Diarrhoea remains a major cause of illness in Papua New Guinea (PNG); however, little is known about its aetiology. As a result of the cholera outbreak that spread throughout PNG in 2009-2011, we conducted diarrhoeal surveillance in Eastern Highlands Province. Methodology: Following informed consent and a brief questionnaire, participants provided a stool sample or duplicate rectal swabs. Samples were tested for common bacterial pathogens Salmonella spp., Shigella spp., Vibrio spp., Campylobacter spp. and Yersinia enterocolitica using established culture methods. Enteric parasites were detected using microscopy. Results: A total of 216 participants were enrolled; where age was recorded, 42% were under 5 years of age, 6.7% were 5 to 17 years of age and 51.3% ≥18 years of age. One or more pathogens were detected in 68 (31.5%) participants, with Shigella (primarily S. flexneri) being the most commonly isolated (47 of 216 participants). Enteric parasites were detected in 23 of the 216 participants, occurring as a co-infection with another pathogen in 12 of 23 cases. No Vibrio cholerae was detected. Shigella isolates were commonly resistant to ampicillin, tetracycline, co-trimoxazole and chloramphenicol. Conclusions: Shigellae, specifically S. flexneri, are important pathogens in the highlands of PNG. While most studies in low-income settings focus on childhood aetiology, we have demonstrated the importance of Shigella in both children and adults. Enteric parasites remain present and presumably contribute to the burden of gastrointestinal illness. While improvements in sanitation and hygiene would help lower the burden of all aetiologies of infectious diarrhoea, additional control strategies targeting Shigella may also be warranted. © 2014 Greenhill et al.
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
- Full Text:
- Reviewed:
- 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
- Full Text:
- Reviewed:
- 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.
Safety and immunogenicity of pneumococcal conjugate vaccines in a high-risk population : A randomized controlled trial of 10-valent and 13-valent pneumococcal conjugate vaccine in Papua New Guinean infants
- Pomat, William, Van Den Biggelaar, Anita, Wana, Sandra, Francis, Jacinta, Solomon, Vela, Greenhill, Andrew, Ford, Rebecca, Orami, Tilda, Passey, Megan, Jacoby, Peter, Kirkham, Lea-Ann, Lehmann, Deborah, Richmond, Peter
- Authors: Pomat, William , Van Den Biggelaar, Anita , Wana, Sandra , Francis, Jacinta , Solomon, Vela , Greenhill, Andrew , Ford, Rebecca , Orami, Tilda , Passey, Megan , Jacoby, Peter , Kirkham, Lea-Ann , Lehmann, Deborah , Richmond, Peter
- Date: 2019
- Type: Text , Journal article
- Relation: Clinical Infectious Diseases Vol. 68, no. 9 (2019), p. 1472-1481
- Full Text:
- Reviewed:
- Description: Background. There are little data on the immunogenicity of PCV10 and PCV13 in the same high-risk population. Methods. PCV10 and PCV13 were studied head-to-head in a randomized controlled trial in Papua New Guinea in which 262 infants received 3 doses of PCV10 or PCV13 at 1, 2, and 3 months of age. Serotype-specific immunoglobulin G (IgG) concentrations, and pneumococcal and nontypeable Haemophilus influenzae (NTHi) carriage were assessed prevaccination and at 4 and 9 months of age. Infants were followed up for safety until 9 months of age. Results. One month after the third dose of PCV10 or PCV13, 80% of infants had IgG concentrations ≥0.35µg/mL for vaccine serotypes, and 6 months postvaccination IgG concentrations ≥0.35 µg/mL were maintained for 8/10 shared PCV serotypes in > 75% of children vaccinated with either PCV10 or PCV13. Children carried a total of 65 different pneumococcal serotypes (plus nonserotypeable). At 4 months of age, 92% (95% confidence interval [CI] 85–96) of children vaccinated with PCV10 and 81% (95% CI 72–88) vaccinated with PCV13 were pneumococcal carriers (P = .023), whereas no differences were seen at 9 months of age, or for NTHi carriage. Both vaccines were well tolerated and not associated with serious adverse events. Conclusions. Infant vaccination with 3 doses of PCV10 or PCV13 is safe and immunogenic in a highly endemic setting; however, to significantly reduce pneumococcal disease in these settings, PCVs with broader serotype coverage and potency to reduce pneumococcal carriage are needed. Clinical Trials Registration. NCT01619462.
- Authors: Pomat, William , Van Den Biggelaar, Anita , Wana, Sandra , Francis, Jacinta , Solomon, Vela , Greenhill, Andrew , Ford, Rebecca , Orami, Tilda , Passey, Megan , Jacoby, Peter , Kirkham, Lea-Ann , Lehmann, Deborah , Richmond, Peter
- Date: 2019
- Type: Text , Journal article
- Relation: Clinical Infectious Diseases Vol. 68, no. 9 (2019), p. 1472-1481
- Full Text:
- Reviewed:
- Description: Background. There are little data on the immunogenicity of PCV10 and PCV13 in the same high-risk population. Methods. PCV10 and PCV13 were studied head-to-head in a randomized controlled trial in Papua New Guinea in which 262 infants received 3 doses of PCV10 or PCV13 at 1, 2, and 3 months of age. Serotype-specific immunoglobulin G (IgG) concentrations, and pneumococcal and nontypeable Haemophilus influenzae (NTHi) carriage were assessed prevaccination and at 4 and 9 months of age. Infants were followed up for safety until 9 months of age. Results. One month after the third dose of PCV10 or PCV13, 80% of infants had IgG concentrations ≥0.35µg/mL for vaccine serotypes, and 6 months postvaccination IgG concentrations ≥0.35 µg/mL were maintained for 8/10 shared PCV serotypes in > 75% of children vaccinated with either PCV10 or PCV13. Children carried a total of 65 different pneumococcal serotypes (plus nonserotypeable). At 4 months of age, 92% (95% confidence interval [CI] 85–96) of children vaccinated with PCV10 and 81% (95% CI 72–88) vaccinated with PCV13 were pneumococcal carriers (P = .023), whereas no differences were seen at 9 months of age, or for NTHi carriage. Both vaccines were well tolerated and not associated with serious adverse events. Conclusions. Infant vaccination with 3 doses of PCV10 or PCV13 is safe and immunogenic in a highly endemic setting; however, to significantly reduce pneumococcal disease in these settings, PCVs with broader serotype coverage and potency to reduce pneumococcal carriage are needed. Clinical Trials Registration. NCT01619462.
Limited impact of neonatal or early infant schedules of 7-valent pneumococcal conjugate vaccination on nasopharyngeal carriage of Streptococcus pneumoniae in Papua New Guinean children: A randomized controlled trial
- Aho, Celestine, Michael, Audrey, Yoannes, Mition, Greenhill, Andrew, Jacoby, Peter, Reeder, John, Pomat, William, Saleu, Gerard, Namuigi, Pioto, Phuanukoonnon, Suparat, Smith-Vaughan, Heidi, Leach, Amanda, Richmond, Peter, Lehmann, Deborah
- Authors: Aho, Celestine , Michael, Audrey , Yoannes, Mition , Greenhill, Andrew , Jacoby, Peter , Reeder, John , Pomat, William , Saleu, Gerard , Namuigi, Pioto , Phuanukoonnon, Suparat , Smith-Vaughan, Heidi , Leach, Amanda , Richmond, Peter , Lehmann, Deborah
- Date: 2016
- Type: Text , Journal article
- Relation: Vaccine Reports Vol. 6, no. (2016), p. 36-43
- Full Text:
- Reviewed:
- Description: Streptococcus pneumoniae is a leading cause of pneumonia, the most common cause of childhood death. Papua New Guinean children experience high rates of nasopharyngeal pneumococcal colonization within weeks of birth, predisposing them to pneumococcal disease. In a trial to determine the safety and immunogenicity of early infant vaccination with 7-valent pneumococcal conjugate vaccine (7vPCV), we investigated the impact of early schedules on pneumococcal carriage. Infants were randomized at birth to receive 7vPCV in a 0–1–2-month (n = 101) or a 1–2–3-month (n = 105) schedule or no 7vPCV (n = 106). All children received 23-valent pneumococcal polysaccharide vaccine at age 9 months. We cultured nasopharyngeal swabs (NPS) collected at ages 1, 2, 3, 4 weeks and 3, 9, 18 months, and middle ear discharge if present. Pneumococcal serotypes were identified by the Quellung reaction. A total of 1761 NPS were cultured. The prevalence of pneumococcal carriage was 22% at 1 week of age, rising to 80% by age 3 months and remained >70% thereafter, with high-density carriage in 42% of pneumococcuspositive samples. We identified 63 different serotypes; 43% of isolates from controls were 13vPCV serotypes. There were no significant differences in 7vPCV serotype carriage between 7vPCV recipients and controls at any age (22% vs. 31% at 9 months, p = 0.2). At age 9 months the prevalence of non-7vPCV carriage was 17% higher in 7vPCV recipients (48%) than in controls (25%, p = 0.02). More non-7vPCV serotypes were isolated from ear discharge in 16 7vPCV recipients than from 4 controls (48% vs. 25%, p = 0.13). The limited impact of neonatal or accelerated infant 7vPCV schedules on vaccine serotype carriage is probably due to the early onset of dense carriage of a broad range of pneumococcal serotypes. While serotype-independent pneumococcal vaccines are needed in high-risk populations, the underlying environmental factors and sources of infection must be investigated.
- Authors: Aho, Celestine , Michael, Audrey , Yoannes, Mition , Greenhill, Andrew , Jacoby, Peter , Reeder, John , Pomat, William , Saleu, Gerard , Namuigi, Pioto , Phuanukoonnon, Suparat , Smith-Vaughan, Heidi , Leach, Amanda , Richmond, Peter , Lehmann, Deborah
- Date: 2016
- Type: Text , Journal article
- Relation: Vaccine Reports Vol. 6, no. (2016), p. 36-43
- Full Text:
- Reviewed:
- Description: Streptococcus pneumoniae is a leading cause of pneumonia, the most common cause of childhood death. Papua New Guinean children experience high rates of nasopharyngeal pneumococcal colonization within weeks of birth, predisposing them to pneumococcal disease. In a trial to determine the safety and immunogenicity of early infant vaccination with 7-valent pneumococcal conjugate vaccine (7vPCV), we investigated the impact of early schedules on pneumococcal carriage. Infants were randomized at birth to receive 7vPCV in a 0–1–2-month (n = 101) or a 1–2–3-month (n = 105) schedule or no 7vPCV (n = 106). All children received 23-valent pneumococcal polysaccharide vaccine at age 9 months. We cultured nasopharyngeal swabs (NPS) collected at ages 1, 2, 3, 4 weeks and 3, 9, 18 months, and middle ear discharge if present. Pneumococcal serotypes were identified by the Quellung reaction. A total of 1761 NPS were cultured. The prevalence of pneumococcal carriage was 22% at 1 week of age, rising to 80% by age 3 months and remained >70% thereafter, with high-density carriage in 42% of pneumococcuspositive samples. We identified 63 different serotypes; 43% of isolates from controls were 13vPCV serotypes. There were no significant differences in 7vPCV serotype carriage between 7vPCV recipients and controls at any age (22% vs. 31% at 9 months, p = 0.2). At age 9 months the prevalence of non-7vPCV carriage was 17% higher in 7vPCV recipients (48%) than in controls (25%, p = 0.02). More non-7vPCV serotypes were isolated from ear discharge in 16 7vPCV recipients than from 4 controls (48% vs. 25%, p = 0.13). The limited impact of neonatal or accelerated infant 7vPCV schedules on vaccine serotype carriage is probably due to the early onset of dense carriage of a broad range of pneumococcal serotypes. While serotype-independent pneumococcal vaccines are needed in high-risk populations, the underlying environmental factors and sources of infection must be investigated.
Nitrogen fixation and nifH diversity in human gut microbiota
- Igai, Katsura, Itakura, Manabu, Nishijima, Suguru, Tsurumaru, Hirohito, Suda, Wataru, Tsutaya, Takumi, Tomitsuka, Eriko, Tadokoro, Kiyoshi, Baba, Jun, Odani, Shingo, Natsuhara, Kazumi, Morita, Ayako, Yoneda, Minoru, Greenhill, Andrew, Horwood, Paul, Inoue, Jun-ichi, Ohkuma, Moriya, Hongoh, Yuichi, Yamamoto, Taro, Siba, Peter, Hattori, Masahira, Minamisawa, Kiwamu, Umezaki, Masahiro
- Authors: Igai, Katsura , Itakura, Manabu , Nishijima, Suguru , Tsurumaru, Hirohito , Suda, Wataru , Tsutaya, Takumi , Tomitsuka, Eriko , Tadokoro, Kiyoshi , Baba, Jun , Odani, Shingo , Natsuhara, Kazumi , Morita, Ayako , Yoneda, Minoru , Greenhill, Andrew , Horwood, Paul , Inoue, Jun-ichi , Ohkuma, Moriya , Hongoh, Yuichi , Yamamoto, Taro , Siba, Peter , Hattori, Masahira , Minamisawa, Kiwamu , Umezaki, Masahiro
- Date: 2016
- Type: Text , Journal article
- Relation: Scientific Reports Vol. 6, no. (2016), p. 1-11
- Full Text:
- Reviewed:
- Description: It has been hypothesized that nitrogen fixation occurs in the human gut. However, whether the gut microbiota truly has this potential remains unclear. We investigated the nitrogen-fixing activity and diversity of the nitrogenase reductase (NifH) genes in the faecal microbiota of humans, focusing on Papua New Guinean and Japanese individuals with low to high habitual nitrogen intake. A 15 N 2 incorporation assay showed significant enrichment of 15 N in all faecal samples, irrespective of the host nitrogen intake, which was also supported by an acetylene reduction assay. The fixed nitrogen corresponded to 0.01% of the standard nitrogen requirement for humans, although our data implied that the contribution in the gut in vivo might be higher than this value. The nifH genes recovered in cloning and metagenomic analyses were classified in two clusters: one comprising sequences almost identical to Klebsiella sequences and the other related to sequences of Clostridiales members. These results are consistent with an analysis of databases of faecal metagenomes from other human populations. Collectively, the human gut microbiota has a potential for nitrogen fixation, which may be attributable to Klebsiella and Clostridiales strains, although no evidence was found that the nitrogen-fixing activity substantially contributes to the host nitrogen balance. © The Author(s) 2016.
- Authors: Igai, Katsura , Itakura, Manabu , Nishijima, Suguru , Tsurumaru, Hirohito , Suda, Wataru , Tsutaya, Takumi , Tomitsuka, Eriko , Tadokoro, Kiyoshi , Baba, Jun , Odani, Shingo , Natsuhara, Kazumi , Morita, Ayako , Yoneda, Minoru , Greenhill, Andrew , Horwood, Paul , Inoue, Jun-ichi , Ohkuma, Moriya , Hongoh, Yuichi , Yamamoto, Taro , Siba, Peter , Hattori, Masahira , Minamisawa, Kiwamu , Umezaki, Masahiro
- Date: 2016
- Type: Text , Journal article
- Relation: Scientific Reports Vol. 6, no. (2016), p. 1-11
- Full Text:
- Reviewed:
- Description: It has been hypothesized that nitrogen fixation occurs in the human gut. However, whether the gut microbiota truly has this potential remains unclear. We investigated the nitrogen-fixing activity and diversity of the nitrogenase reductase (NifH) genes in the faecal microbiota of humans, focusing on Papua New Guinean and Japanese individuals with low to high habitual nitrogen intake. A 15 N 2 incorporation assay showed significant enrichment of 15 N in all faecal samples, irrespective of the host nitrogen intake, which was also supported by an acetylene reduction assay. The fixed nitrogen corresponded to 0.01% of the standard nitrogen requirement for humans, although our data implied that the contribution in the gut in vivo might be higher than this value. The nifH genes recovered in cloning and metagenomic analyses were classified in two clusters: one comprising sequences almost identical to Klebsiella sequences and the other related to sequences of Clostridiales members. These results are consistent with an analysis of databases of faecal metagenomes from other human populations. Collectively, the human gut microbiota has a potential for nitrogen fixation, which may be attributable to Klebsiella and Clostridiales strains, although no evidence was found that the nitrogen-fixing activity substantially contributes to the host nitrogen balance. © The Author(s) 2016.
Wild Australian birds and drug-resistant bacteria : Characterisation of antibiotic-resistant Escherichia coli and Enterococcus spp
- Smith, Hannah, Clarke, Rohan, Larkins, Jo-Ann, Bean, David, Greenhill, Andrew
- Authors: Smith, Hannah , Clarke, Rohan , Larkins, Jo-Ann , Bean, David , Greenhill, Andrew
- Date: 2019
- Type: Text , Journal article
- Relation: Emu-Austral Ornithology Vol. 119, no. 4 (2019), p. 384-390
- Full Text:
- Reviewed:
- Description: Birds can spread microorganisms through their movement; however, it is still not fully understood how wild birds acquire and disperse antimicrobial-resistant (AMR) bacteria. We sampled wild Australian birds from three geographically distinct locations for the presence of AMR strains of two clinically important species of bacteria, Escherichia coli and Enterococcus spp. A total of 121 birds were sampled, representing 15 different species. Thirty E. coli and 54 Enterococcus isolates were tested for resistance to 12 and 8 different antibiotics, respectively. Resistance to at least one antibiotic was common, being detected in 96% of Enterococcus and 60% of E. coli isolates. The vancomycin-resistance genes vanA and vanD were detected in 22% of enterococci (13% vanA, 9% vanD), while 9% displayed phenotypic resistance with no associated gene. Wild birds are a carrier of AMR bacteria in Australia, and are capable of harbouring a more diverse range of vancomycin-resistance genes than is typically seen among Australian clinical isolates.
- Authors: Smith, Hannah , Clarke, Rohan , Larkins, Jo-Ann , Bean, David , Greenhill, Andrew
- Date: 2019
- Type: Text , Journal article
- Relation: Emu-Austral Ornithology Vol. 119, no. 4 (2019), p. 384-390
- Full Text:
- Reviewed:
- Description: Birds can spread microorganisms through their movement; however, it is still not fully understood how wild birds acquire and disperse antimicrobial-resistant (AMR) bacteria. We sampled wild Australian birds from three geographically distinct locations for the presence of AMR strains of two clinically important species of bacteria, Escherichia coli and Enterococcus spp. A total of 121 birds were sampled, representing 15 different species. Thirty E. coli and 54 Enterococcus isolates were tested for resistance to 12 and 8 different antibiotics, respectively. Resistance to at least one antibiotic was common, being detected in 96% of Enterococcus and 60% of E. coli isolates. The vancomycin-resistance genes vanA and vanD were detected in 22% of enterococci (13% vanA, 9% vanD), while 9% displayed phenotypic resistance with no associated gene. Wild birds are a carrier of AMR bacteria in Australia, and are capable of harbouring a more diverse range of vancomycin-resistance genes than is typically seen among Australian clinical isolates.