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3. Genomic epidemiology of Salmonella Typhi in Central Division, Fiji, 2012 to 2016

Author

Davies, Mark R., Duchene, Sebastian, Valcanis, Mary, Jenkins, Aaron P., Jenney, Adam, Rosa, Varanisese, Hayes, Andrew J., Strobel, Aneley Getahun, McIntyre, Liam, Lacey, Jake A., Klemm, Elizabeth J., Wong, Vanessa K., Sahukhan, Aalisha, Thomson, Helen, Page, Andrew, Hocking, Dianna, Wang, Nancy, Tudravu, Litia, Rafai, Eric, Dougan, Gordon, Howden, Benjamin P., Crump, John A., Mulholland, Kim, and Strugnell, Richard A.

Published
2022
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4. Genomic epidemiology and phenotypic characterisation of Salmonella enterica serovar Panama in Victoria, Australia.

Author

Thakur, Samriddhi, Baines, Sarah L., Sia, Cheryll M., Valcanis, Mary, Judd, Louise M., Howden, Benjamin P., Newton, Hayley J., and Ingle, Danielle J.

Subjects
SALMONELLA enterica, MULTIDRUG resistance, DRUG resistance in microorganisms, DRUG resistance, SALMONELLA diseases, SALMONELLA food poisoning, TYPHOID fever
Abstract

Salmonella enterica serovar Panama, a causative agent of non-typhoidal salmonellosis (NTS), is one of several serovars that causes invasive NTS disease (iNTS) in humans. S. Panama is an understudied pathogen, with its pathobiology poorly understood. It is a predominant iNTS serovar in Australia, a high-income country with high rates of salmonellosis, where S. Panama has been documented to have a high odds ratio (13.9–15.26) for causing iNTS. This study investigates the genomic epidemiology and antimicrobial resistance profiles of all S. Panama isolates recovered in Victoria, Australia, between 2000 and 2021. We examined the infection dynamics of S. Panama in seven isolates, representing the genetic diversity of the study population. Two sub-lineages, encompassed within a previously described Asian lineage, were identified. Multi-drug resistance (resistance to ≥3 drug classes) was detected in 46 (51.7%) Australian isolates. The plasmid-mediated colistin resistance gene, mcr1.1, was detected in one Australian S. Panama isolate, carried by an IncI plasmid previously reported in Salmonella and Escherichia coli isolates collected from poultry in South-East Asia. Examination of the intracellular replication dynamics of S. Panama isolates demonstrated diverse phenotypes. In THP-1 derived macrophages, despite low host cell uptake, S. Panama showed higher replication rates over time compared to S. enterica serovar Typhimurium. However, a causative genotype could not be identified to explain this observed phenotype. This study provides insights into the S. Panama isolates circulating in Australia over two-decades, finding that 78% were linked to international travel suggesting importation in Australia. It shows MDR was common in this iNTS serovar, and colistin resistance reported for the first time. It provides the first data on the host-pathogen interactions of S. Panama in Australia, which will aid our collective understanding of the pathobiology of S. Panama and iNTS serovars more broadly. Author summary: In Australia, non-typhoidal Salmonella (NTS) cases have been on the rise since the 1970s; characterised by self-limiting enteritis, some NTS infections can result in systemic infections called invasive NTS disease. Salmonella enterica serovar Panama is a leading iNTS serovar in Australia. This study characterised the genomic epidemiology of S. Panama, identifying two lineages circulating in Australia over two decades and placing them within a global context. It also investigated the antimicrobial resistance (AMR) mechanisms of S. Panama, with multi-drug resistance commonly observed. Further, it identified the first plasmid-mediated colistin-resistant S. Panama in Australia. We additionally examined the characteristics of S. Panama-mediated host-pathogen interactions in both epithelial and macrophage cells lines, providing the first insight into the infection dynamics of this understudied pathogen. Thus, this study combines genomics and in vitro infection experiments to understand the pathogenic behaviour of the neglected iNTS S. Panama. [ABSTRACT FROM AUTHOR]

Published
2024
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5. Multistate Outbreak of Salmonella enterica Serovar Heidelberg with Unidentified Source, Australia, 2018-2019

Author

Kerr, Elenor J., Stafford, Russell, Rathnayake, Irani U., Graham, Rikki M.A., Fearnley, Emily, Gregory, Joy, Glasgow, Keira, Wright, Rose, Sintchenko, Vitali, Wang, Qinning, Howard, Peter, Leong, Lex E.X., Valcanis, Mary, Pitchers, William, Lambert, Stephen B., and Jennison, Amy V.

Subjects
Epidemics -- Statistics -- Causes of -- Australia, Salmonella -- Identification and classification -- Distribution -- Genetic aspects, Salmonellosis -- Statistics -- Causes of, Company distribution practices, Health
Abstract

Salmonella enterica serovar Heidelberg is a frequently identified serotype among infections in humans in North America, East Africa, and Asia but is uncommon in Australia. An average of 37 cases [...]

Published
2022
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9. Genetic heterogeneity in theSalmonellaTyphi Vi capsule locus: A population genomic study from Fiji

Author

Getahun Strobel, Aneley, primary, Hayes, Andrew J., additional, Wirth, Wytamma, additional, Mua, Mikaele, additional, Saumalua, Tiko, additional, Cabenatabua, Orisi, additional, Soqo, Vika, additional, Rosa, Varanisese, additional, Wang, Nancy, additional, Lacey, Jake A., additional, Hocking, Dianna, additional, Valcanis, Mary, additional, Jenney, Adam, additional, Howden, Benjamin P., additional, Duchene, Sebastian, additional, Mulholland, Kim, additional, Strugnell, Richard A., additional, and Davies, Mark R., additional

Published
2023
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11. Source attribution of campylobacteriosis in Australia, 2017–2019

Author

McLure, Angus, primary, Smith, James J., additional, Firestone, Simon Matthew, additional, Kirk, Martyn D., additional, French, Nigel, additional, Fearnley, Emily, additional, Wallace, Rhiannon, additional, Valcanis, Mary, additional, Bulach, Dieter, additional, Moffatt, Cameron R.M., additional, Selvey, Linda A., additional, Jennison, Amy, additional, Cribb, Danielle M., additional, and Glass, Kathryn, additional

Published
2023
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13. Global diversity and antimicrobial resistance of typhoid fever pathogens:Insights from a meta-analysis of 13,000 Salmonella Typhi genomes

Author

Carey, Megan E, Dyson, Zoe A, Ingle, Danielle J, Amir, Afreenish, Aworh, Mabel K, Chattaway, Marie Anne, Chew, Ka Lip, Crump, John A, Feasey, Nicholas A, Howden, Benjamin P, Keddy, Karen H, Maes, Mailis, Parry, Christopher M, Van Puyvelde, Sandra, Webb, Hattie E, Afolayan, Ayorinde Oluwatobiloba, Alexander, Anna P, Anandan, Shalini, Andrews, Jason R, Ashton, Philip M, Basnyat, Buddha, Bavdekar, Ashish, Bogoch, Isaac I, Clemens, John D, da Silva, Kesia Esther, De, Anuradha, de Ligt, Joep, Diaz Guevara, Paula Lucia, Dolecek, Christiane, Dutta, Shanta, Ehlers, Marthie M, Francois Watkins, Louise, Garrett, Denise O, Godbole, Gauri, Gordon, Melita A, Greenhill, Andrew R, Griffin, Chelsey, Gupta, Madhu, Hendriksen, Rene S, Heyderman, Robert S, Hooda, Yogesh, Hormazabal, Juan Carlos, Ikhimiukor, Odion O, Iqbal, Junaid, Jacob, Jobin John, Jenkins, Claire, Jinka, Dasaratha Ramaiah, John, Jacob, Kang, Gagandeep, Kanteh, Abdoulie, Kapil, Arti, Karkey, Abhilasha, Kariuki, Samuel, Kingsley, Robert A, Koshy, Roshine Mary, Lauer, AC, Levine, Myron M, Lingegowda, Ravikumar Kadahalli, Luby, Stephen P, Mackenzie, Grant Austin, Mashe, Tapfumanei, Msefula, Chisomo, Mutreja, Ankur, Nagaraj, Geetha, Nagaraj, Savitha, Nair, Satheesh, Naseri, Take K, Nimarota-Brown, Susana, Njamkepo, Elisabeth, Okeke, Iruka N, Perumal, Sulochana Putli Bai, Pollard, Andrew J, Pragasam, Agila Kumari, Qadri, Firdausi, Qamar, Farah N, Rahman, Sadia Isfat Ara, Rambocus, Savitra Devi, Rasko, David A, Ray, Pallab, Robins-Browne, Roy, Rongsen-Chandola, Temsunaro, Rutanga, Jean Pierre, Saha, Samir K, Saha, Senjuti, Saigal, Karnika, Sajib, Mohammad Saiful Islam, Seidman, Jessica C, Shakya, Jivan, Shamanna, Varun, Shastri, Jayanthi, Shrestha, Rajeev, Sia, Sonia, Sikorski, Michael J, Singh, Ashita, Smith, Anthony M, Tagg, Kaitlin A, Tamrakar, Dipesh, Tanmoy, Arif Mohammed, Thomas, Maria, Thomas, Mathew S, Thomsen, Robert, Thomson, Nicholas R, Tupua, Siaosi, Vaidya, Krista, Valcanis, Mary, Veeraraghavan, Balaji, Weill, François-Xavier, Wright, Jackie, Dougan, Gordon, Argimón, Silvia, Keane, Jacqueline A, Aanensen, David M, Baker, Stephen, Holt, Kathryn E, Carey, Megan E, Dyson, Zoe A, Ingle, Danielle J, Amir, Afreenish, Aworh, Mabel K, Chattaway, Marie Anne, Chew, Ka Lip, Crump, John A, Feasey, Nicholas A, Howden, Benjamin P, Keddy, Karen H, Maes, Mailis, Parry, Christopher M, Van Puyvelde, Sandra, Webb, Hattie E, Afolayan, Ayorinde Oluwatobiloba, Alexander, Anna P, Anandan, Shalini, Andrews, Jason R, Ashton, Philip M, Basnyat, Buddha, Bavdekar, Ashish, Bogoch, Isaac I, Clemens, John D, da Silva, Kesia Esther, De, Anuradha, de Ligt, Joep, Diaz Guevara, Paula Lucia, Dolecek, Christiane, Dutta, Shanta, Ehlers, Marthie M, Francois Watkins, Louise, Garrett, Denise O, Godbole, Gauri, Gordon, Melita A, Greenhill, Andrew R, Griffin, Chelsey, Gupta, Madhu, Hendriksen, Rene S, Heyderman, Robert S, Hooda, Yogesh, Hormazabal, Juan Carlos, Ikhimiukor, Odion O, Iqbal, Junaid, Jacob, Jobin John, Jenkins, Claire, Jinka, Dasaratha Ramaiah, John, Jacob, Kang, Gagandeep, Kanteh, Abdoulie, Kapil, Arti, Karkey, Abhilasha, Kariuki, Samuel, Kingsley, Robert A, Koshy, Roshine Mary, Lauer, AC, Levine, Myron M, Lingegowda, Ravikumar Kadahalli, Luby, Stephen P, Mackenzie, Grant Austin, Mashe, Tapfumanei, Msefula, Chisomo, Mutreja, Ankur, Nagaraj, Geetha, Nagaraj, Savitha, Nair, Satheesh, Naseri, Take K, Nimarota-Brown, Susana, Njamkepo, Elisabeth, Okeke, Iruka N, Perumal, Sulochana Putli Bai, Pollard, Andrew J, Pragasam, Agila Kumari, Qadri, Firdausi, Qamar, Farah N, Rahman, Sadia Isfat Ara, Rambocus, Savitra Devi, Rasko, David A, Ray, Pallab, Robins-Browne, Roy, Rongsen-Chandola, Temsunaro, Rutanga, Jean Pierre, Saha, Samir K, Saha, Senjuti, Saigal, Karnika, Sajib, Mohammad Saiful Islam, Seidman, Jessica C, Shakya, Jivan, Shamanna, Varun, Shastri, Jayanthi, Shrestha, Rajeev, Sia, Sonia, Sikorski, Michael J, Singh, Ashita, Smith, Anthony M, Tagg, Kaitlin A, Tamrakar, Dipesh, Tanmoy, Arif Mohammed, Thomas, Maria, Thomas, Mathew S, Thomsen, Robert, Thomson, Nicholas R, Tupua, Siaosi, Vaidya, Krista, Valcanis, Mary, Veeraraghavan, Balaji, Weill, François-Xavier, Wright, Jackie, Dougan, Gordon, Argimón, Silvia, Keane, Jacqueline A, Aanensen, David M, Baker, Stephen, and Holt, Kathryn E

Abstract

Background: The Global Typhoid Genomics Consortium was established to bring together the typhoid research community to aggregate and analyse Salmonella enterica serovar Typhi (Typhi) genomic data to inform public health action. This analysis, which marks 22 years since the publication of the first Typhi genome, represents the largest Typhi genome sequence collection to date (n=13,000). Methods: This is a meta-analysis of global genotype and antimicrobial resistance (AMR) determinants extracted from previously sequenced genome data and analysed using consistent methods implemented in open analysis platforms GenoTyphi and Pathogenwatch. Results: Compared with previous global snapshots, the data highlight that genotype 4.3.1 (H58) has not spread beyond Asia and Eastern/Southern Africa; in other regions, distinct genotypes dominate and have independently evolved AMR. Data gaps remain in many parts of the world, and we show the potential of travel-associated sequences to provide informal 'sentinel' surveillance for such locations. The data indicate that ciprofloxacin non-susceptibility (>1 resistance determinant) is widespread across geographies and genotypes, with high-level ciprofloxacin resistance (≥3 determinants) reaching 20% prevalence in South Asia. Extensively drug-resistant (XDR) typhoid has become dominant in Pakistan (70% in 2020) but has not yet become established elsewhere. Ceftriaxone resistance has emerged in eight non-XDR genotypes, including a ciprofloxacin-resistant lineage (4.3.1.2.1) in India. Azithromycin resistance mutations were detected at low prevalence in South Asia, including in two common ciprofloxacin-resistant genotypes. Conclusions: The consortium's aim is to encourage continued data sharing and collaboration to monitor the emergence and global spread of AMR Typhi, and to inform decision-making around the introduction of typhoid conjugate vaccines (TCVs) and other prevention and control s

Published
2023

16. Dissecting the molecular evolution of fluoroquinolone-resistant Shigella sonnei

Author

Chung The, Hao, Boinett, Christine, Pham Thanh, Duy, Jenkins, Claire, Weill, Francois-Xavier, Howden, Benjamin P., Valcanis, Mary, De Lappe, Niall, Cormican, Martin, Wangchuk, Sonam, Bodhidatta, Ladaporn, Mason, Carl J., Nguyen, To Nguyen Thi, Ha Thanh, Tuyen, Voong, Vinh Phat, Duong, Vu Thuy, Nguyen, Phu Huong Lan, Turner, Paul, Wick, Ryan, Ceyssens, Pieter-Jan, Thwaites, Guy, Holt, Kathryn E., Thomson, Nicholas R., Rabaa, Maia A., and Baker, Stephen

Published
2019
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18. Intercontinental dissemination of azithromycin-resistant shigellosis through sexual transmission: a cross-sectional study

Author

Baker, Kate S, Dallman, Timothy J, Ashton, Philip M, Day, Martin, Hughes, Gwenda, Crook, Paul D, Gilbart, Victoria L, Zittermann, Sandra, Allen, Vanessa G, Howden, Benjamin P, Tomita, Takehiro, Valcanis, Mary, Harris, Simon R, Connor, Thomas R, Sintchenko, Vitali, Howard, Peter, Brown, Jeremy D, Petty, Nicola K, Gouali, Malika, Thanh, Duy Pham, Keddy, Karen H, Smith, Anthony M, Talukder, Kaisar A, Faruque, Shah M, Parkhill, Julian, Baker, Stephen, Weill, François-Xavier, Jenkins, Claire, and Thomson, Nicholas R

Published
2015
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19. Persistence of Rare Salmonella Typhi Genotypes Susceptible to First-Line Antibiotics in the Remote Islands of Samoa

Author

Sikorski, Michael J., primary, Hazen, Tracy H., additional, Desai, Sachin N., additional, Nimarota-Brown, Susana, additional, Tupua, Siaosi, additional, Sialeipata, Michelle, additional, Rambocus, Savitra, additional, Ingle, Danielle J., additional, Duchene, Sebastian, additional, Ballard, Susan A., additional, Valcanis, Mary, additional, Zufan, Sara, additional, Ma, Jianguo, additional, Sahl, Jason W., additional, Maes, Mailis, additional, Dougan, Gordon, additional, Thomsen, Robert E., additional, Robins-Browne, Roy M., additional, Howden, Benjamin P., additional, Naseri, Take K., additional, Levine, Myron M., additional, and Rasko, David A., additional

Published
2022
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20. Spatial-temporal and phylogenetic analyses of epidemiologic data to help understand the modes of transmission of endemic typhoid fever in Samoa

Author

Sikorski, Michael J., primary, Ma, Jianguo, additional, Hazen, Tracy H., additional, Desai, Sachin N., additional, Tupua, Siaosi, additional, Nimarota-Brown, Susana, additional, Sialeipata, Michelle, additional, Rambocus, Savitra, additional, Ballard, Susan A., additional, Valcanis, Mary, additional, Thomsen, Robert E., additional, Robins-Browne, Roy M., additional, Howden, Benjamin P., additional, Naseri, Take K., additional, Levine, Myron M., additional, and Rasko, David A., additional

Published
2022
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21. Genomic epidemiology of Salmonella Typhi in Central Division, Fiji, 2012 to 2016

Author

Davies, Mark R, Duchene, Sebastian, Valcanis, Mary, Jenkins, Aaron P, Jenney, Adam, Rosa, Varanisese, Hayes, Andrew J, Strobel, Aneley Getahun, McIntyre, Liam, Lacey, Jake A, Klemm, Elizabeth J, Wong, Vanessa K, Sahukhan, Aalisha, Thomson, Helen, Page, Andrew, Hocking, Dianna, Wang, Nancy, Tudravu, Litia, Rafai, Eric, Dougan, Gordon, Howden, Benjamin P, Crump, John A, Mulholland, Kim, Strugnell, Richard A, Dougan, Gordon [0000-0003-0022-965X], and Apollo - University of Cambridge Repository

Subjects
Public health, Fiji, Outbreak, Population genomics, Bayesian, Phylodynamics, Salmonella Typhi, Phylogeny, Typhoid fever
Abstract

BACKGROUND: Typhoid fever is endemic in some Pacific Island Countries including Fiji and Samoa yet genomic surveillance is not routine in such settings. Previous studies suggested imports of the global H58 clade of Salmonella enterica var Typhi (Salmonella Typhi) contribute to disease in these countries which, given the MDR potential of H58, does not auger well for treatment. The objective of the study was to define the genomic epidemiology of Salmonella Typhi in Fiji. METHODS: Genomic sequencing approaches were implemented to study the distribution of 255 Salmonella Typhi isolates from the Central Division of Fiji. We augmented epidemiological surveillance and Bayesian phylogenomic approaches with a multi-year typhoid case-control study to define geospatial patterns among typhoid cases. FINDINGS: Genomic analyses showed Salmonella Typhi from Fiji resolved into 2 non-H58 genotypes with isolates from the two dominant ethnic groups, the Indigenous (iTaukei) and non-iTaukei genetically indistinguishable. Low rates of international importation of clones was observed and overall, there were very low levels an antibiotic resistance within the endemic Fijian typhoid genotypes. Genomic epidemiological investigations were able to identify previously unlinked case clusters. Bayesian phylodynamic analyses suggested that genomic variation within the larger endemic Salmonella Typhi genotype expanded at discreet times, then contracted. INTERPRETATION: Cyclones and flooding drove 'waves' of typhoid outbreaks in Fiji which, through population aggregation, poor sanitation and water safety, and then mobility of the population, spread clones more widely. Minimal international importations of new typhoid clones suggest that targeted local intervention strategies may be useful in controlling endemic typhoid infection. These findings add to our understanding of typhoid transmission networks in an endemic island country with broad implications, particularly across Pacific Island Countries. FUNDING: This work was supported by the Coalition Against Typhoid through the Bill and Melinda Gates Foundation [grant number OPP1017518], the Victorian Government, the National Health and Medical Research Council Australia, the Australian Research Council, and the Fiji Ministry of Health and Medical Services.

Published
2022
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22. Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events

Author

Wong, Vanessa K, Baker, Stephen, Pickard, Derek J, Parkhill, Julian, Page, Andrew J, Feasey, Nicholas A, Kingsley, Robert A, Thomson, Nicholas R, Keane, Jacqueline A, Weill, François-Xavier, Edwards, David J, Hawkey, Jane, Harris, Simon R, Mather, Alison E, Cain, Amy K, Hadfield, James, Hart, Peter J, Thieu, Nga Tran Vu, Klemm, Elizabeth J, Glinos, Dafni A, Breiman, Robert F, Watson, Conall H, Kariuki, Samuel, Gordon, Melita A, Heyderman, Robert S, Okoro, Chinyere, Jacobs, Jan, Lunguya, Octavie, Edmunds, W John, Msefula, Chisomo, Chabalgoity, Jose A, Kama, Mike, Jenkins, Kylie, Dutta, Shanta, Marks, Florian, Campos, Josefina, Thompson, Corinne, Obaro, Stephen, MacLennan, Calman A, Dolecek, Christiane, Keddy, Karen H, Smith, Anthony M, Parry, Christopher M, Karkey, Abhilasha, Mulholland, E Kim, Campbell, James I, Dongol, Sabina, Basnyat, Buddha, Dufour, Muriel, Bandaranayake, Don, Naseri, Take Toleafoa, Singh, Shalini Pravin, Hatta, Mochammad, Newton, Paul, Onsare, Robert S, Isaia, Lupeoletalalei, Dance, David, Davong, Viengmon, Thwaites, Guy, Wijedoru, Lalith, Crump, John A, De Pinna, Elizabeth, Nair, Satheesh, Nilles, Eric J, Thanh, Duy Pham, Turner, Paul, Soeng, Sona, Valcanis, Mary, Powling, Joan, Dimovski, Karolina, Hogg, Geoff, Farrar, Jeremy, Holt, Kathryn E, and Dougan, Gordon

Published
2015
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23. Source attribution of campylobacteriosis in Australia circa 2018

Author

McLure, Angus, primary, Smith, James J, additional, Firestone, Simon Matthew, additional, Kirk, Martyn D, additional, French, Nigel, additional, Fearnley, Emily, additional, Wallace, Rhiannon, additional, Valcanis, Mary, additional, Bulach, Dieter, additional, Moffatt, Cameron, additional, Selvey, Linda A, additional, Jennison, Amy, additional, and Glass, Kathryn, additional

Published
2022
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24. Additional file 6 of Risk factors for campylobacteriosis in Australia: outcomes of a 2018–2019 case–control study

Author

Cribb, Danielle M., Varrone, Liana, Wallace, Rhiannon L., McLure, Angus T., Smith, James J., Stafford, Russell J., Bulach, Dieter M., Selvey, Linda A., Firestone, Simon M., French, Nigel P., Valcanis, Mary, Fearnley, Emily J., Sloan-Gardner, Timothy S., Graham, Trudy, Glass, Kathryn, and Kirk, Martyn D.

Abstract

Additional file 6: Sensitivity analysis of final multivariable model for participants that consumed chicken with adjusted odds ratios (aORs) together with 95% confidence intervals (95% CI) showing exposures associated with an increased or decreased risk of campylobacteriosis.

Published
2022
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25. Additional file 2 of Risk factors for campylobacteriosis in Australia: outcomes of a 2018–2019 case–control study

Author

Cribb, Danielle M., Varrone, Liana, Wallace, Rhiannon L., McLure, Angus T., Smith, James J., Stafford, Russell J., Bulach, Dieter M., Selvey, Linda A., Firestone, Simon M., French, Nigel P., Valcanis, Mary, Fearnley, Emily J., Sloan-Gardner, Timothy S., Graham, Trudy, Glass, Kathryn, and Kirk, Martyn D.

Abstract

Additional file 2: Age and sex distribution of study cases (n = 571) compared to notified cases of campylobacteriosis in Australia in 2018 (n = 33,129) and 2019 (n = 36,131)*.

Published
2022
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26. Additional file 1 of Risk factors for campylobacteriosis in Australia: outcomes of a 2018–2019 case–control study

Author

Cribb, Danielle M., Varrone, Liana, Wallace, Rhiannon L., McLure, Angus T., Smith, James J., Stafford, Russell J., Bulach, Dieter M., Selvey, Linda A., Firestone, Simon M., French, Nigel P., Valcanis, Mary, Fearnley, Emily J., Sloan-Gardner, Timothy S., Graham, Trudy, Glass, Kathryn, and Kirk, Martyn D.

Abstract

Additional file 1: Process for logistic regression model selection for all campylobacteriosis, Campylobacter jejuni, and Campylobacter coli sensitivity analysis.

Published
2022
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28. Genomic diversity of antimicrobial resistance in non-typhoidal Salmonella in Victoria, Australia

Author

Sia, Cheryll M., primary, Baines, Sarah L., additional, Valcanis, Mary, additional, Lee, Darren Y. J., additional, Gonçalves da Silva, Anders, additional, Ballard, Susan A., additional, Easton, Marion, additional, Seemann, Torsten, additional, Howden, Benjamin P., additional, Ingle, Danielle J., additional, and Williamson, Deborah A., additional

Published
2021
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29. Genomic Epidemiology and Antimicrobial Resistance Mechanisms of Imported Typhoid in Australia

Author

Ingle, Danielle J., primary, Andersson, Patiyan, additional, Valcanis, Mary, additional, Wilmot, Mathilda, additional, Easton, Marion, additional, Lane, Courtney, additional, Barden, Jessica, additional, Gonçalves da Silva, Anders, additional, Seemann, Torsten, additional, Horan, Kristy, additional, Ballard, Susan A., additional, Sherry, Norelle L., additional, Williamson, Deborah A., additional, and Howden, Benjamin P., additional

Published
2021
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30. Investigating the Source of SalmonellaAgona Contamination in Australian Feed Mills Using Core Genome Phylogenetic Analysis

Author

Parker, Elizabeth Mary, Valcanis, Mary, Andersson, Patiyan, and Wittum, Thomas E.

Abstract

Salmonella entericaserovar Agona is commonly detected in raw animal feed components during routine microbial monitoring of Australian commercial animal feed mills. We hypothesized that Salmonella-contaminated raw feed components originate at the rendering or oil seed crushing plant and are distributed to mills in different locations. Our objective was to investigate the source of SalmonellaAgona contaminated raw feed components. Whole genome sequences of 37 SalmonellaAgona isolates, 36 from raw feed components and 1 from finished feed, collected from 10 Australian feed mills located in 4 Australian states, were compared using core genome phylogenetic analysis. After DNA extraction and de novodraft assembly of the paired reads, the draft genomes were aligned using conserved signature indel phylogeny against a reference genome for SalmonellaAgona, to identify single nucleotide polymorphisms in the core genome. Five distinct clades corresponding to the five different suppliers of SalmonellaAgona-contaminated raw feed components were identified in the resulting phylogenetic tree. The results also provided evidence of cross-transference of SalmonellaAgona between canola meal, meat meal, and finished feed within a mill. Core genome phylogenetic analysis facilitated tracing the source of Salmonellacontamination in feed mills.

Published
2023
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32. Antimicrobial Resistance of Campylobacter spp. Causing Human Infection in Australia: An International Comparison

Author

Wallace, Rhiannon, Bulach, Dieter, McLure, Angus, Varrone, Liana, Jennison, Amy, Valcanis, Mary, Smith, James, Polkinghorne, Benjamin, Glass, Kathryn, Kirk, Martyn, Wallace, Rhiannon, Bulach, Dieter, McLure, Angus, Varrone, Liana, Jennison, Amy, Valcanis, Mary, Smith, James, Polkinghorne, Benjamin, Glass, Kathryn, and Kirk, Martyn

Abstract

The study investigates the prevalence of antimicrobial resistance in Campylobacter jejuni and Campylobacter coli in gastroenteritis patients in the eight most populous regions in Australia and compares the prevalence of antimicrobial resistance in Europe and North America. A total of 164 Campylobacter isolates were collected from patients with campylobacteriosis and tested for susceptibility to six antimicrobials using ETEST® strips and compared with reports from Europe and the United States. Genomes were sequenced on Illumina NextSeq to identify genetic determinants of resistance. Phenotypically, 1.8%, 14.0%, 14.6%, and 20.1% of isolates were resistant to erythromycin (ERY), ampicillin, tetracycline (TET), and ciprofloxacin (CIP), respectively. Comparing published phenotypic results of antimicrobial resistance in several European countries and the United States with these Australian isolates reveals that rates observed in Australia are among the lowest observed for ERY, CIP, and TET for both C. coli and C. jejuni. For each antimicrobial tested, concordance between resistance phenotype and genotype ranged from 66.6% to 100.0%. This study highlights that, among industrialized countries, Portugal and Spain have very high levels of antimicrobial resistance in C. jejuni and C. coli, especially when compared with the United Kingdom, United States, and Australia.

Published
2021

35. Molecular characterization of Campylobacter spp. recovered from beef, chicken, lamb and pork products at retail in Australia

Author

Wallace, Rhiannon, Bulach, Dieter, Jennison, Amy V., Valcanis, Mary, McLure, Angus, Smith, James J, Graham, Trudy, SAPUTRA, THEMY, Firestone, Simon, SYMES, SALLY, Waters, Natasha, STYLIANOPOULOS, ANASTASIA, Kirk, Martyn, Glass, Katie, Wallace, Rhiannon, Bulach, Dieter, Jennison, Amy V., Valcanis, Mary, McLure, Angus, Smith, James J, Graham, Trudy, SAPUTRA, THEMY, Firestone, Simon, SYMES, SALLY, Waters, Natasha, STYLIANOPOULOS, ANASTASIA, Kirk, Martyn, and Glass, Katie

Abstract

Australian rates of campylobacteriosis are among the highest in developed countries, yet only limited work has been done to characterize Campylobacter spp. in Australian retail products. We performed whole genome sequencing (WGS) on 331 C. coli and 285 C. jejuni from retail chicken meat, as well as beef, chicken, lamb and pork offal (organs). Campylobacter isolates were highly diverse, with 113 sequence types (STs) including 38 novel STs, identified from 616 isolates. Genomic analysis suggests very low levels (2.3-15.3%) of resistance to aminoglycoside, beta-lactam, fluoroquinolone, macrolide and tetracycline antibiotics. A majority (>90%) of isolates (52/56) possessing the fluoroquinolone resistance-associated T86I mutation in the gyrA gene belonged to ST860, ST2083 or ST7323. The 44 pork offal isolates were highly diverse, representing 33 STs (11 novel STs) and harboured genes associated with resistance to aminoglycosides, lincosamides and macrolides not generally found in isolates from other sources. Prevalence of multidrug resistant genotypes was very low (<5%), but ten-fold higher in C. coli than C. jejuni. This study highlights that Campylobacter spp. from retail products in Australia are highly genotypically diverse and important differences in antimicrobial resistance exist between Campylobacter species and animal sources.

Published
2020

36. Low-level fluoroquinolone resistance among campylobacter jejuni isolates in Australia

Author

Unicomb, Leanne E., Ferguson, John, Stafford, Russell J., Ashbolt, Rosie, Kirk, Martyn D., Becker, Niels G., Patel, Mahomed S., Gilbert, Gwendolyn L., Valcanis, Mary, and Mickan, Lance

Subjects
Campylobacter -- Research, Campylobacter -- Physiological aspects, Campylobacter -- Demographic aspects, Health, Health care industry
Published
2006

39. Prolonged Outbreak of Multidrug-Resistant Shigella sonnei Harboring bla CTX-M-27 in Victoria, Australia

Author

Ingle, Danielle J., primary, Andersson, Patiyan, additional, Valcanis, Mary, additional, Barnden, Jessica, additional, da Silva, Anders Gonçalves, additional, Horan, Kristy A., additional, Seemann, Torsten, additional, Easton, Marion, additional, Williamson, Deborah A., additional, Sherry, Norelle L., additional, and Howden, Benjamin P., additional

Published
2020
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41. Molecular characterization of Campylobacter spp. recovered from beef, chicken, lamb and pork products at retail in Australia

Author

Wallace, Rhiannon L., primary, Bulach, Dieter M., additional, Jennison, Amy V., additional, Valcanis, Mary, additional, McLure, Angus, additional, Smith, James J., additional, Graham, Trudy, additional, Saputra, Themy, additional, Firestone, Simon, additional, Symes, Sally, additional, Waters, Natasha, additional, Stylianopoulos, Anastasia, additional, Kirk, Martyn D., additional, and Glass, Kathryn, additional

Published
2020
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42. South Asia as a Reservoir for the Global Spread of Ciprofloxacin-Resistant Shigella sonnei: A Cross-Sectional Study

Author

Chung The, Hao, Rabaa, Maia A., Pham Thanh, Duy, De Lappe, Niall, Cormican, Martin, Valcanis, Mary, Howden, Benjamin P., Wangchuk, Sonam, Bodhidatta, Ladaporn, Mason, Carl J., Nguyen Thi Nguyen, To, Vu Thuy, Duong, Thompson, Corinne N., Phu Huong Lan, Nguyen, Voong Vinh, Phat, Ha Thanh, Tuyen, Turner, Paul, Sar, Poda, Thwaites, Guy, Thomson, Nicholas R., Holt, Kathryn E., and Baker, Stephen

Subjects
Mutation -- Research, Public health -- Analysis, Shigella sonnei -- Research, Diarrhea -- Care and treatment, Ciprofloxacin -- Usage, Biological sciences
Abstract

Background Antimicrobial resistance is a major issue in the Shigellae, particularly as a specific multidrug-resistant (MDR) lineage of Shigella sonnei (lineage III) is becoming globally dominant. Ciprofloxacin is a recommended treatment for Shigella infections. However, ciprofloxacin-resistant S. sonnei are being increasingly isolated in Asia and sporadically reported on other continents. We hypothesized that Asia is a primary hub for the recent international spread of ciprofloxacin-resistant S. sonnei. Methods and Findings We performed whole-genome sequencing on a collection of 60 contemporaneous ciprofloxacin-resistant S. sonnei isolated in four countries within Asia (Vietnam, n = 11; Bhutan, n = 12; Thailand, n = 1; Cambodia, n = 1) and two outside of Asia (Australia, n = 19; Ireland, n = 16). We reconstructed the recent evolutionary history of these organisms and combined these data with their geographical location of isolation. Placing these sequences into a global phylogeny, we found that all ciprofloxacin-resistant S. sonnei formed a single clade within a Central Asian expansion of lineage III. Furthermore, our data show that resistance to ciprofloxacin within S. sonnei may be globally attributed to a single clonal emergence event, encompassing sequential gyrA-S83L, parC-S80I, and gyrA-D87G mutations. Geographical data predict that South Asia is the likely primary source of these organisms, which are being regularly exported across Asia and intercontinentally into Australia, the United States and Europe. Our analysis was limited by the number of S. sonnei sequences available from diverse geographical areas and time periods, and we cannot discount the potential existence of other unsampled reservoir populations of antimicrobial-resistant S. sonnei. Conclusions This study suggests that a single clone, which is widespread in South Asia, is likely driving the current intercontinental surge of ciprofloxacin-resistant S. sonnei and is capable of establishing endemic transmission in new locations. Despite being limited in geographical scope, our work has major implications for understanding the international transfer of antimicrobial-resistant pathogens, with S. sonnei acting as a tractable model for studying how antimicrobial-resistant Gram-negative bacteria spread globally., Author(s): Hao Chung The 1, Maia A. Rabaa 1,2, Duy Pham Thanh 1, Niall De Lappe 3, Martin Cormican 4, Mary Valcanis 5, Benjamin P. Howden 5, Sonam Wangchuk 6, [...]

Published
2016
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43. Status of antimicrobial resistance in clinical isolates of Campylobacter jejuni and Campylobacter coli in Australia

Author

Wallace, Rhiannon L., Bulach, Deiter, McLure, Angus, Varrone, Liana, Jennison, Amy V., Valcanis, Mary, Smith, James J., Polkiinghorne, Benjamin G, Glass, Kathryn, and Kirk, Martyn D.

Subjects
060408 Genomics, 060501 Bacteriology, 111706 Epidemiology, erm(B), Antibiotic resistance, ciprofloxacin, erythromycin, whole genome sequencing (WGS), Campylobacter, 060502 Infectious Agents, tetracycline
Abstract

The aim of this study was to investigate the prevalence of resistance to six antimicrobials in Campylobacter jejuni and Campylobacter coli isolates from gastroenteritis cases using phenotypic antimicrobial susceptibility testing (AST) and whole genome sequencing (WGS). Resistance rates in Australia were compared to European Food Safety Authority data (EFSA) and the United States Centers for Disease Control and Prevention’s (CDC) National Antimicrobial Resistance Monitoring System. A total of 164 Campylobacter isolates (137 C. jejuni and 27 C. coli) were collected from patients with campylobacteriosis from eight Australian states and territories from October 2018 to February 2019 and tested for susceptibility to six antimicrobials using ETEST® strips. Genomic DNA was sequenced using the Illumina NextSeq platform and resistance genes identified from assembled WGS sequences using the Nullarbor pipeline and ResFinder. Phenotypically, 14.0%, 20.1%, 1.8% and 14.6% of isolates were resistant to ampicillin, ciprofloxacin, erythromycin and tetracycline, respectively. All isolates tested were susceptible to amoxicillin-clavulanic acid and gentamicin with no resistance detected. We identified twelve resistance genes, namely aad9, aadE, aph(3’)Illa, blaOXA-61, blaOXA-184, blaOXA-185, blaOXA-449, blaOXA-625, catA, erm(B), sat4, tet(O), and mutations in the gyrA and 23S rRNA genes. For each antimicrobial tested, concordance between resistance phenotype and genotype ranged from 33.3 to 100.0%. Compared to the United States and countries in Europe, Australia has low rates of ciprofloxacin and tetracycline resistance. Although one in five isolates were resistant to ciprofloxacin, most (98.2%) were susceptible to erythromycin, the drug of choice for treating Campylobacter infection.

Published
2019

45. Co-circulation of Multidrug-resistant Shigella Among Men Who Have Sex With Men in Australia

Author

Ingle, Danielle, Easton, Marion, Valcanis, Mary, Seemann, Torsten, Kwong, Jason, Stephens, Nicola, Carter, Glen P., da Silva, Anders Gonçalves, Adamopoulos, Jim, Baines, Sarah L., Holt, Kathryn E., Kirk, Martyn, Ingle, Danielle, Easton, Marion, Valcanis, Mary, Seemann, Torsten, Kwong, Jason, Stephens, Nicola, Carter, Glen P., da Silva, Anders Gonçalves, Adamopoulos, Jim, Baines, Sarah L., Holt, Kathryn E., and Kirk, Martyn

Abstract

In urban Australia, the burden of shigellosis is either in returning travellers from shigellosis-endemic regions, or in men who have sex with men (MSM). Here, we combine genomic data with comprehensive epidemiological data on sexual exposure and travel to describe the spread of multidrug-resistant Shigella lineages.

Published
2019

48. Co-circulation of Multidrug-resistant Shigella Among Men Who Have Sex With Men in Australia

Author

Ingle, Danielle J, primary, Easton, Marion, additional, Valcanis, Mary, additional, Seemann, Torsten, additional, Kwong, Jason C, additional, Stephens, Nicola, additional, Carter, Glen P, additional, Gonçalves da Silva, Anders, additional, Adamopoulos, James, additional, Baines, Sarah L, additional, Holt, Kathryn E, additional, Chow, Eric P F, additional, Fairley, Christopher K, additional, Chen, Marcus Y, additional, Kirk, Martyn D, additional, Howden, Benjamin P, additional, and Williamson, Deborah A, additional

Published
2019
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50. Seven Salmonella Typhimurium Outbreaks in Australia Linked by Trace-Back and Whole Genome Sequencing

Author

Ford, Laura, primary, Wang, Qinning, additional, Stafford, Russell, additional, Ressler, Kelly-Anne, additional, Norton, Sophie, additional, Shadbolt, Craig, additional, Hope, Kirsty, additional, Franklin, Neil, additional, Krsteski, Radomir, additional, Carswell, Adrienne, additional, Carter, Glen P., additional, Seemann, Torsten, additional, Howard, Peter, additional, Valcanis, Mary, additional, Castillo, Cristina Fabiola Sotomayor, additional, Bates, John, additional, Glass, Kathryn, additional, Williamson, Deborah A., additional, Sintchenko, Vitali, additional, Howden, Benjamin P., additional, and Kirk, Martyn D., additional

Published
2018
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