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Article ; Online: Extensive epigenetic modification with large-scale chromosomal and plasmid recombination characterise the Legionella longbeachae serogroup 1 genome

Sandy Slow / Trevor Anderson / David R. Murdoch / Samuel Bloomfield / David Winter / Patrick J. Biggs

Scientific Reports, Vol 12, Iss 1, Pp 1-

2022 Volume 13

Abstract: Abstract Legionella longbeachae is an environmental bacterium that is the most clinically significant Legionella species in New Zealand (NZ), causing around two-thirds of all notified cases of Legionnaires’ disease. Here we report the sequencing and ... ...

Abstract	Abstract Legionella longbeachae is an environmental bacterium that is the most clinically significant Legionella species in New Zealand (NZ), causing around two-thirds of all notified cases of Legionnaires’ disease. Here we report the sequencing and analysis of the geo-temporal genetic diversity of 54 L. longbeachae serogroup 1 (sg1) clinical isolates, derived from cases from around NZ over a 22-year period, including one complete genome and its associated methylome. The 54 sg1 isolates belonged to two main clades that last shared a common ancestor between 95 BCE and 1694 CE. There was diversity at the genome-structural level, with large-scale arrangements occurring in some regions of the chromosome and evidence of extensive chromosomal and plasmid recombination. This includes the presence of plasmids derived from recombination and horizontal gene transfer between various Legionella species, indicating there has been both intra- and inter-species gene flow. However, because similar plasmids were found among isolates within each clade, plasmid recombination events may pre-empt the emergence of new L. longbeachae strains. Our complete NZ reference genome consisted of a 4.1 Mb chromosome and a 108 kb plasmid. The genome was highly methylated with two known epigenetic modifications, m4C and m6A, occurring in particular sequence motifs within the genome.
Keywords	Medicine ; R ; Science ; Q
Subject code	580
Language	English
Publishing date	2022-04-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Legionellosis Caused by Non- Legionella pneumophila Species, with a Focus on Legionella longbeachae

Stephen T. Chambers / Sandy Slow / Amy Scott-Thomas / David R. Murdoch

Microorganisms, Vol 9, Iss 2, p

2021 Volume 291

Abstract: Although known as causes of community-acquired pneumonia and Pontiac fever, the global burden of infection caused by Legionella species other than Legionella pneumophila is under-recognised. Non- L. pneumophila legionellae have a worldwide distribution, ... ...

Abstract	Although known as causes of community-acquired pneumonia and Pontiac fever, the global burden of infection caused by Legionella species other than Legionella pneumophila is under-recognised. Non- L. pneumophila legionellae have a worldwide distribution, although common testing strategies for legionellosis favour detection of L. pneumophila over other Legionella species, leading to an inherent diagnostic bias and under-detection of cases. When systematically tested for in Australia and New Zealand, L. longbeachae was shown to be a leading cause of community-acquired pneumonia. Exposure to potting soils and compost is a particular risk for infection from L. longbeachae , and L. longbeachae may be better adapted to soil and composting plant material than other Legionella species. It is possible that the high rate of L. longbeachae reported in Australia and New Zealand is related to the composition of commercial potting soils which, unlike European products, contain pine bark and sawdust. Genetic studies have demonstrated that the Legionella genomes are highly plastic, with areas of the chromosome showing high levels of recombination as well as horizontal gene transfer both within and between species via plasmids. This, combined with various secretion systems and extensive effector repertoires that enable the bacterium to hijack host cell functions and resources, is instrumental in shaping its pathogenesis, survival and growth. Prevention of legionellosis is hampered by surveillance systems that are compromised by ascertainment bias, which limits commitment to an effective public health response. Current prevention strategies in Australia and New Zealand are directed at individual gardeners who use potting soils and compost. This consists of advice to avoid aerosols generated by the use of potting soils and use masks and gloves, but there is little evidence that this is effective. There is a need to better understand the epidemiology of L. longbeachae and other Legionella species in order to develop effective ...
Keywords	L. longbeachae ; Legionella ; epidemiology ; environment ; pathogenesis ; prevention ; Biology (General) ; QH301-705.5
Subject code	580
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Etiology of Severe Febrile Illness in Low- and Middle-Income Countries

Namrata Prasad / David R Murdoch / Hugh Reyburn / John A Crump

PLoS ONE, Vol 10, Iss 6, p e

A Systematic Review.

2015 Volume 0127962

Abstract: With apparent declines in malaria worldwide during the last decade and more widespread use of malaria rapid diagnostic tests, healthcare workers in low-resource areas face a growing proportion of febrile patients without malaria. We sought to describe ... ...

Abstract	With apparent declines in malaria worldwide during the last decade and more widespread use of malaria rapid diagnostic tests, healthcare workers in low-resource areas face a growing proportion of febrile patients without malaria. We sought to describe current knowledge and identify information gaps of the etiology severe febrile illness in low-and middle-income countries.We conducted a systematic review of studies conducted in low-and-middle income countries 1980-2013 that prospectively assessed consecutive febrile patients admitted to hospital using rigorous laboratory-based case definitions. We found 45 eligible studies describing 54,578 patients; 9,771 (17.9%) had a positive result for ≥1 pathogen meeting diagnostic criteria. There were no eligible studies identified from Southern and Middle Africa, Eastern Asia, Oceania, Latin American and Caribbean regions, and the European region. The median (range) number of diagnostic tests meeting our confirmed laboratory case definitions was 2 (1 to 11) per study. Of diagnostic tests, 5,052 (10.3%) of 49,143 had confirmed bacterial or fungal bloodstream infection; 709 (3.8%) of 18,142 had bacterial zoonosis; 3,488 (28.5%) of 12,245 had malaria; and 1,804 (17.4%) of 10,389 had a viral infection.We demonstrate a wide range of pathogens associated with severe febrile illness and highlight the substantial information gaps regarding the geographic distribution and role of common pathogens. High quality severe febrile illness etiology research that is comprehensive with respect to pathogens and geographically representative is needed.
Keywords	Medicine ; R ; Science ; Q
Subject code	610
Language	English
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Whole-genome sequencing and ad hoc shared genome analysis of Staphylococcus aureus isolates from a New Zealand primary school

Pippa Scott / Ji Zhang / Trevor Anderson / Patricia C. Priest / Stephen Chambers / Helen Smith / David R. Murdoch / Nigel French / Patrick J. Biggs

Scientific Reports, Vol 11, Iss 1, Pp 1-

2021 Volume 11

Abstract: Abstract Epidemiological studies of communicable diseases increasingly use large whole-genome sequencing (WGS) datasets to explore the transmission of pathogens. It is important to obtain an initial overview of datasets and identify closely related ... ...

Abstract	Abstract Epidemiological studies of communicable diseases increasingly use large whole-genome sequencing (WGS) datasets to explore the transmission of pathogens. It is important to obtain an initial overview of datasets and identify closely related isolates, but this can be challenging with large numbers of isolates and imperfect sequencing. We used an ad hoc whole-genome multi locus sequence typing method to summarise data from a longitudinal study of Staphylococcus aureus in a primary school in New Zealand. Each pair of isolates was compared and the number of genes where alleles differed between isolates was tallied to produce a matrix of “allelic differences”. We plotted histograms of the number of allelic differences between isolates for: all isolate pairs; pairs of isolates from different individuals; and pairs of isolates from the same individual. 340 sequenced isolates were included, and the ad hoc shared genome contained 445 genes. There were between 0 and 420 allelic differences between isolate pairs and the majority of pairs had more than 260 allelic differences. We found many genetically closely related S. aureus isolates from single individuals and a smaller number of closely-related isolates from separate individuals. Multiple S. aureus isolates from the same individual were usually very closely related or identical over the ad hoc shared genome. Siblings carried genetically similar, but not identical isolates. An ad hoc shared genome approach to WGS analysis can accommodate imperfect sequencing of the included isolates, and can provide insights into relationships between isolates in epidemiological studies with large WGS datasets containing diverse isolates.
Keywords	Medicine ; R ; Science ; Q
Subject code	580
Language	English
Publishing date	2021-10-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Global health classroom

Roshit K. Bothara / Malama Tafuna’i / Tim J. Wilkinson / Jen Desrosiers / Susan Jack / Philip K. Pattemore / Tony Walls / Faafetai Sopoaga / David R. Murdoch / Andrew P. Miller

Globalization and Health, Vol 17, Iss 1, Pp 1-

mixed methods evaluation of an interinstitutional model for reciprocal global health learning among Samoan and New Zealand medical students

2021 Volume 14

Abstract: Abstract Background Global health education partnerships should be collaborative and reciprocal to ensure mutual benefit. Utilisation of digital technologies can overcome geographic boundaries and facilitate collaborative global health learning. Global ... ...

Abstract	Abstract Background Global health education partnerships should be collaborative and reciprocal to ensure mutual benefit. Utilisation of digital technologies can overcome geographic boundaries and facilitate collaborative global health learning. Global Health Classroom (GHCR) is a collaborative global health learning model involving medical students from different countries learning about each other’s health systems, cultures, and determinants of health via videoconference. Principles of reciprocity and interinstitutional partnership informed the development of the GHCR. This study explores learning outcomes and experiences in the GHCR between students from New Zealand and Samoa. Methods This study used a mixed methods approach employing post-GHCR questionnaires and semi-structured face-to-face interviews to explore self-reported learning and experiences among medical students in the GHCR. The GHCR collaboration studied was between the medical schools at the University of Otago, New Zealand and the National University of Samoa, Samoa. Results Questionnaire response rate was 85% (74/87). Nineteen interviews were conducted among New Zealand and Samoan students. Students reported acquiring the intended learning outcomes relating to patient care, health systems, culture, and determinants of health with regards to their partner country. Interview data was indicative of attitudinal changes in relation to cultural humility and curiosity. Some reported a vision for progress regarding their own health system. Students in the GHCR reported that learning with their international peers in the virtual classroom made learning about global health more real and tangible. The benefits to students from both countries indicated reciprocity. Conclusions This study demonstrates GHCR to be a promising model for collaborative and reciprocal global health learning using a student-led format and employing digital technology to create a virtual classroom. The self-reported learning outcomes align favourably with those recommended in the ...
Keywords	Global health education ; Digital technology ; Videoconferencing ; Partnership ; Collaboration ; Public aspects of medicine ; RA1-1270
Subject code	360
Language	English
Publishing date	2021-09-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Interactions of staphyloxanthin and enterobactin with myeloperoxidase and reactive chlorine species

Coker, Melanie S / Anthony J. Kettle / Christine C. Winterbourn / David R. Murdoch / Louisa V. Forbes / Matthew Plowman-Holmes

Archives of biochemistry and biophysics. 2018 May 15, v. 646

2018

Abstract: When neutrophils engulf bacteria, myeloperoxidase converts hydrogen peroxide to hypochlorous acid, which is toxic to all micro-organisms. It has been suggested that some pathogens have virulence factors that target myeloperoxidase to dampen the oxidative ...

Abstract	When neutrophils engulf bacteria, myeloperoxidase converts hydrogen peroxide to hypochlorous acid, which is toxic to all micro-organisms. It has been suggested that some pathogens have virulence factors that target myeloperoxidase to dampen the oxidative reactions of neutrophils. These virulence factors include staphyloxanthin, the golden pigment of Staphylococcus aureus, and enterobactin – a siderophore released by gram-negative bacteria. We investigated the potential of staphyloxanthin and enterobactin to shield bacteria from hypochlorous acid and related chloramines. Clinical strains of S. aureus with high levels of staphyloxanthin and related carotenoids were in general more resistant to low doses of hypochlorous acid than non-pigmented bacteria. But some non-pigmented strains were also resistant to the oxidant. Doses of reactive chlorine species that killed bacteria also bleached their carotenoids. Hypochlorous acid, NH2Cl, and NHCl2 bleached purified staphyloxanthin. When S. aureus were phagocytosed by neutrophils there was no discernible loss of staphyloxanthin. These data suggest that staphyloxanthin is capable of protecting bacteria from low doses of reactive chlorine species formed inside phagosomes. Enterobactin was not an inhibitor of myeloperoxidase. We conclude that staphyloxanthin may protect some bacterial strains against oxidative killing by neutrophils, but enterobactin will not inhibit the production of hypochlorous acid.
Keywords	carotenoids ; chlorine ; enterobactin ; enzyme inhibitors ; Gram-negative bacteria ; hydrogen peroxide ; myeloperoxidase ; neutrophils ; oxidants ; pathogens ; phagosomes ; siderophores ; Staphylococcus aureus ; toxicity ; virulence
Language	English
Dates of publication	2018-0515
Size	p. 80-89.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	523-x
ISSN	1096-0384 ; 0003-9861
ISSN (online)	1096-0384
ISSN	0003-9861
DOI	10.1016/j.abb.2018.03.039
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: A prospective study of bloodstream infections among febrile adolescents and adults attending Yangon General Hospital, Yangon, Myanmar.

Tin Ohn Myat / Khine Mar Oo / Hla Kye Mone / Wah Win Htike / Ambarish Biswas / Rachel F Hannaway / David R Murdoch / James E Ussher / John A Crump

PLoS Neglected Tropical Diseases, Vol 14, Iss 4, p e

2020 Volume 0008268

Abstract: Data on causes of community-onset bloodstream infection in Myanmar are scarce. We aimed to identify etiological agents of bloodstream infections and patterns of antimicrobial resistance among febrile adolescents and adults attending Yangon General ... ...

Abstract	Data on causes of community-onset bloodstream infection in Myanmar are scarce. We aimed to identify etiological agents of bloodstream infections and patterns of antimicrobial resistance among febrile adolescents and adults attending Yangon General Hospital (YGH), Yangon, Myanmar. We recruited patients ≥12 years old with fever ≥38°C who attended YGH from 5 October 2015 through 4 October 2016. A standardized clinical history and physical examination was performed. Provisional diagnoses and vital status at discharge was recorded. Blood was collected for culture, bloodstream isolates were identified, and antimicrobial susceptibility testing was performed. Using whole-genome sequencing, we identified antimicrobial resistance mechanisms of Enterobacteriaceae and sequence types of Enterobacteriaceae and Streptococcus agalactiae. Among 947 participants, 90 (9.5%) had bloodstream infections (BSI) of which 82 (91.1%) were of community-onset. Of 91 pathogens isolated from 90 positive blood cultures, we identified 43 (47.3%) Salmonella enterica including 33 (76.7%) serovar Typhi and 10 (23.3%) serovar Paratyphi A; 20 (22.0%) Escherichia coli; 7 (7.7%) Klebsiella pneumoniae; 6 (6.6%), Staphylococcus aureus; 4 (4.4%) yeasts; and 1 (1.1%) each of Burkholderia pseudomallei and Streptococcus agalactiae. Of 70 Enterobacteriaceae, 62 (88.6%) were fluoroquinolone-resistant. Among 27 E. coli and K. pneumoniae, 18 (66.6%) were extended-spectrum beta-lactamase (ESBL)-producers, and 1 (3.7%) each were AmpC beta-lactamase- and carbapenemase-producers. Fluoroquinolone resistance was associated predominantly with mutations in the quinolone resistance-determining region. blaCTX-M-15 expression was common among ESBL-producers. Methicillin-resistant S. aureus was not detected. Fluoroquinolone-resistant, but not multiple drug-resistant, typhoidal S. enterica was the leading cause of community-onset BSI at a tertiary hospital in Yangon, Myanmar. Fluoroquinolone and extended-spectrum cephalosporin resistance was common among other ...
Keywords	Arctic medicine. Tropical medicine ; RC955-962 ; Public aspects of medicine ; RA1-1270
Language	English
Publishing date	2020-04-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: One Health Aotearoa

Sarah Harrison / Michael G. Baker / Jackie Benschop / Russell G. Death / Nigel P. French / Garth Harmsworth / Robin J. Lake / Iain L. Lamont / Patricia C. Priest / James E. Ussher / David R. Murdoch

One Health Outlook, Vol 2, Iss 1, Pp 1-

a transdisciplinary initiative to improve human, animal and environmental health in New Zealand

2020 Volume 6

Abstract: Abstract There is increased recognition that complex health challenges at the human-animal-environmental interface require a transdisciplinary, “whole-of-society” approach. This philosophy is particularly pertinent in Aotearoa-New Zealand because of the ... ...

Abstract	Abstract There is increased recognition that complex health challenges at the human-animal-environmental interface require a transdisciplinary, “whole-of-society” approach. This philosophy is particularly pertinent in Aotearoa-New Zealand because of the country’s relatively isolated island ecosystem, economic reliance on agriculture and its intensification, and existing indigenous worldview that emphasises holism and interconnectivity between humans, animals and the environment. In New Zealand, the One Health Aotearoa (OHA) alliance was established in order to better connect researchers and to address a growing number of infectious diseases challenges. The emphasis of OHA is to bring together and facilitate interactions between people from diverse disciplines, link to stakeholders and communities, and engage with policy-makers, government operational agencies, and funders, thus providing a holistic and integrative systems-thinking approach to address priority questions and achieve desired outcomes in One Health. The initial focus of OHA has been on infectious diseases, but there is increasing recognition of the potential benefits of the alliance to address broader complex issues. Greater involvement and overlap of the environmental sciences, human and animal health sciences, social science, and indigenous kaupapa Māori research is particularly critical for ensuring its success within the New Zealand context. Given the economic and cultural importance of New Zealand’s “clean, green” image, a One Health approach that draws strongly on the environmental sciences makes particular sense. Furthermore, as the global environment becomes increasingly stressed by anthropogenic pressures our research may hold potential solutions for similar challenges elsewhere.
Keywords	One health ; New Zealand ; Ecosystem ; Indigenous ; Infectious diseases ; Environmental sciences ; GE1-350 ; Public aspects of medicine ; RA1-1270
Subject code	360
Language	English
Publishing date	2020-01-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Risk Factors for Legionella longbeachae Legionnaires’ Disease, New Zealand

Emma Kenagy / Patricia C. Priest / Claire M. Cameron / Debbie Smith / Pippa Scott / Vicki Cho / Peter Mitchell / David R. Murdoch

Emerging Infectious Diseases, Vol 23, Iss 7, Pp 1148-

2017 Volume 1154

Abstract: Legionella longbeachae, found in soil and compost-derived products, is a globally underdiagnosed cause of Legionnaires’ disease. We conducted a case–control study of L. longbeachae Legionnaires’ disease in Canterbury, New Zealand. Case-patients were ... ...

Abstract	Legionella longbeachae, found in soil and compost-derived products, is a globally underdiagnosed cause of Legionnaires’ disease. We conducted a case–control study of L. longbeachae Legionnaires’ disease in Canterbury, New Zealand. Case-patients were persons hospitalized with L. longbeachae pneumonia, and controls were persons randomly sampled from the electoral roll for the area served by the participating hospital. Among 31 cases and 172 controls, risk factors for Legionnaires’ disease were chronic obstructive pulmonary disease, history of smoking >10 years, and exposure to compost or potting mix. Gardening behaviors associated with L. longbeachae disease included having unwashed hands near the face after exposure to or tipping and troweling compost or potting mix. Mask or glove use was not protective among persons exposed to compost-derived products. Precautions against inhaling compost and attention to hand hygiene might effectively prevent L. longbeachae disease. Long-term smokers and those with chronic obstructive pulmonary disease should be particularly careful.
Keywords	Legionnaires’ disease ; Legionella longbeachae ; risk factors ; compost ; gardening ; parasites ; Medicine ; R ; Infectious and parasitic diseases ; RC109-216
Subject code	610
Language	English
Publishing date	2017-07-01T00:00:00Z
Publisher	Centers for Disease Control and Prevention
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Making standards for quantitative real-time pneumococcal PCR

Susan C. Morpeth / Jim F. Huggett / David R. Murdoch / J. Anthony G. Scott

Biomolecular Detection and Quantification, Vol 2, Iss C, Pp 1-

2014 Volume 3

Abstract: Quantitative lytA PCR is often performed using in-house standards. We hypothesised equivalence when measuring a standard suspension of Streptococcus pneumoniae by colony-forming-units (CFU) or genome-copies. Median (IQR) ratio of CFU/genome-copies was 0 ... ...

Abstract	Quantitative lytA PCR is often performed using in-house standards. We hypothesised equivalence when measuring a standard suspension of Streptococcus pneumoniae by colony-forming-units (CFU) or genome-copies. Median (IQR) ratio of CFU/genome-copies was 0.19 (0.1–1.2). Genome-copies were less variable than CFU, but the discrepancy between the methods highlights challenges with absolute quantification.
Keywords	Quantitative ; Real-time PCR ; Streptococcus pneumoniae ; Standards ; Biology (General) ; QH301-705.5 ; Microbiology ; QR1-502
Language	English
Publishing date	2014-12-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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