Stephen R Ritchie

• University of Auckland

Fluorescent pseudomonads represent one of the largest groups of bacteria inhabiting the surfaces of plants, but their genetic composition in planta is poorly understood. Here, we examined the population structure and diversity of fluorescent pseudomonads isolated from sugar beet grown at two geographic locations (Oxford, United Kingdom and Auckland...

Background Antimicrobial stewardship (AMS) requires a multidisciplinary approach to address the global emergence of antimicrobial resistance (AMR). Nurses have potential roles to influence appropriate antibiotic use. Objective The objective of the study was to investigate knowledge of registered nurses (RNs) on antibiotics, AMR and their understan...

Background: High-output enterostomies and enteroatmospheric fistulas are common causes of intestinal failure, and may necessitate parenteral nutrition and prolonged hospital stay. Reinfusing lost chyme into the distal gut is known to be beneficial, but implementation has been limited because manual reinfusion is unpleasant and labour-intensive, an...

Background When considering antimicrobial stewardship (AMS) interventions, pediatrics is an important and often overlooked group. By 5 years of age, 97% of New Zealand (NZ) children have received antibiotics (median 8 antibiotic courses/child). Prescribing is complex due to age and weight-based adjustments, unpalatable oral preparations and inappro...

Many doctors prescribe antibiotics for a cold, to meet patient’s expectations. As a result, patient’s education about antibiotics and antibiotic resistance forms a major component of the WHO’s Global Action Plan on Antimicrobial Resistance. However, it is not known whether simple educational material can change a person’s attitudes about antibiotic...

Background Antibiotic prescribing for patients with urinary tract infections (UTIs) is often inconsistent with published guidelines. Pharmacists have a key role in the multidisciplinary team to improve the prescribing of antibiotics. Aim This study determined the reasons for low guideline adherence and investigated the effects of a pharmacist‐led,...

Background Mobile phone apps have been shown to enhance guideline adherence by prescribers, but have not been widely evaluated for their impact on guideline adherence by prescribers caring for inpatients with infections. Objectives To determine whether providing the Auckland City Hospital (ACH) antibiotic guidelines in a mobile phone app increased...

Background: The Dundee classification is a simple severity assessment tool that could optimize treatment decisions and clinical outcomes in adult patients with cellulitis; however, it has not been validated in a large cohort. Objectives: To determine whether the Dundee classification reliably identified those patients with cellulitis who had a h...

New Zealand children suffer from high rates of skin and soft tissue infection (SSTI). Staphylococcus aureus colonisation is known to increase the risk of nosocomial infection. We aimed to determine whether S. aureus colonisation also increased the risk of community-onset SSTI. This study, performed within the Growing Up in New Zealand cohort, used...

Aim: The aim of this research was to survey patients' experience of the care provided by the outpatient intravenous antibiotic (OPIVA) service at Auckland City Hospital. Background: Research in Australia has demonstrated that OPIVA is a safe and effective option for managing selected patients who require a long period of intravenous antibiotic trea...

Aim: For patients requiring haemodialysis, the risk of S. aureus disease is higher in those colonised and persists while the person requires haemodialysis, necessitating frequent decolonisation. However, the duration of successful decolonisation is not known. This study aimed to determine the duration of efficacy of decolonisation in intermittent...

Background: In Australia, community-associated methicillin-resistant Staphylococcus aureus (MRSA) lineage sequence type (ST) 93 has rapidly risen to dominance since being described in the early 1990s. We examined 459 ST93 genome sequences from Australia, New Zealand, Samoa, and Europe to investigate the evolutionary history of ST93, its emergence i...

Terminal recombination events. Terminal recombination events (unique to each sequence type) detected with Gubbins in the progressiveMauve core genome alignment (2,157,328 sites). (A) Length distribution of unique recombinant events demonstrating a majority of short recombination events (average: 2,209 base pairs) detected in ST93. (B) Total base pa...

Additional pair-wise nucleotide divergence comparisons between representative S. aureus genomes including ST93. Pair-wise nucleotide divergence across a 10,000 bp sliding window along the S. aureus core genome with comparisons between ST59-ST121, ST93-ST59, ST93-ST8, ST59-ST8, and ST8-ST5. Bases affected by recombination as detected by Gubbins acro...

Details of 459 ST93 Staphylococcus aureus genomes.

Coding sequences in highly divergent regions of ST93. The divergence peaks in Figure 1 were determined using a sliding window of 10,000 bp to assess divergence between the pairwise combinations of sequence types. These annotated genes are extracted from each plateau (i.e., 10,000 bp of divergent peak) and from pairwise combinations involving ST93 w...

Pan-genome details from Roary output.

Source of isolates. (A) Depicts the location from where the isolates originated with red boxes representing states and territories of Australia. European countries include England (n = 45), Scotland (n = 12), Denmark (n = 4), France (n = 1), and Italy (n = 1). Note, Samoan isolates (n = 4) are not depicted. The number of MSSA isolates sequenced, by...

Details of Staphylococcus aureus genomes used to determine phylogenetic position of ST93.

Recombinant regions across Staphylococcus aureus as detected by Gubbins. Maximum-likelihood cladograms (RAxML, GTR+G) of the progressiveMauve (2,157,328 sites, 358,325 SNPs) core alignment after removing recombinant segments (blocks). Recombinant segments were filtered by length as indicated and represent shared ancestral events (red) and events un...

Evidence of short transmission chains in the United Kingdom. Maximum clade credibility tree as in Figure 1, but with transmission chains from the United Kingdom highlighted. Box 1 – four isolates from three individuals of which two were siblings. Box 2 – three isolates from separate patients in same pediatric hospital. Box 3 – there were no obvious...

Network clusters of ST93. (A) General network clusters using the low-resolution fast-greedy modularity optimization algorithm. (B) Cluster assignments were mapped back to the phylogeny.

Non-synonymous mutations restricted to the branch defining the New Zealand clade.

Proportion of methicillin-resistant Staphylococcus aureus that are ST93-MRSA. This represents longitudinal data of ongoing MRSA typing data from Australia, New Zealand (NZ) and United Kingdom (UK). Graph depicts the percentage of MRSA isolates that are ST93 between 2008 and 2015. Data were obtained from Public Health England, United Kingdom, the In...

This article describes the roles of nurses in antimicrobial stewardship, highlighting the need for further education of these roles among registered nurses in New Zealand. This also highlights antimicrobial resistance in New Zealand and the need to address it in a multidisciplinary context, with nurses as advocates and leaders in preventing develop...

Purpose: Antimicrobial stewardship or safe antimicrobial management refers to a multidisciplinary approach to combat the growing problem of antimicrobial resistance associated with antibiotic overprescribing (Infectious Diseases Society of America, 2015; World Health Organization, 2015). The role of registered nurses in AMS is not well understood....

Background Patient-directed education that aims to lower patients’ expectations for antibiotics is a promising strategy to reduce antibiotic usage for viral upper respiratory tract infections (URTI). We aimed to test three posters on a patient population to see whether the messages were comparable in reducing expectations for antibiotics to treat U...

Dipstick urinalysis is an informative, quick, cost-effective and non-invasive diagnostic tool that is useful in clinical practice for the diagnosis of urinary tract infections (UTIs), kidney diseases, and diabetes. We used dipstick urinalysis as a hands-on microbiology laboratory exercise to reinforce student learning about UTIs with a particular f...

Objectives: Staphylococcus aureus skin and soft tissue infection (Sa-SSTI) places a significant burden on healthcare systems. New Zealand has a high incidence of Sa-SSTI, and here most morbidity is caused by a polyclonal methicillin-susceptible (MSSA) population. However, MSSA also colonise asymptomatically the cornified epithelia of approximately...

What is known and objective: Interventions intended to slow the emergence and spread of antibacterial resistance through enhanced antimicrobial stewardship will be more effective if informed by an accurate knowledge of current patterns of antibacterial consumption. For example, knowledge of the relative magnitude of community antibacterial consump...

Background: Patients' expectations may influence prescribers' decisions about antibiotic prescribing for upper respiratory tract infection (URTI). We examined whether a history of an antibiotic related adverse drug reaction (aADR) influenced a person's perception about the safety of antibiotics or their expectation of receiving an antibiotic presc...

Background: Increasing concerns about antibiotic resistance and microbiome disruption have stimulated interest in describing antibiotic consumption in young children. Young children are an age group for whom antibiotics are frequently prescribed. Objectives: To describe community antibiotic dispensing during the first 5 years of life in a large,...

Aim: Infectious disease (ID) hospitalisation rates are increasing in New Zealand (NZ), especially in pre-school children, and Māori and Pacific people. We aimed to identify risk factors for ID hospitalisation in infancy within a birth cohort of NZ children, and to identify differences in risk factors between ethnic groups. Methods: We investigat...

Background: Current guidelines recommend that women with HIV infection receive annual cervical smears. Methods: We evaluated the uptake of annual cervical smears by women with HIV infection under the care of the Infectious Disease Service at Auckland City Hospital. In an attempt to identify potential barriers to regularly receiving an annual cer...

Introduction: The anterior nares are regarded as the primary site for Staphylococcus aureus colonization, although studies have highlighted the potential importance of colonization at extra-nasal sites, including the oropharynx. Accordingly, the aims of this study were to assess the prevalence, persistence and molecular epidemiology of S. aureus c...

New Zealand has unenviably high rates of bacterial resistance to topical antimicrobials. In this Viewpoint, we review the history and usage of topical antimicrobials in New Zealand, and suggest some strategies to mitigate further increases in antimicrobial resistance to topical agents.

The prevalence of fusidic acid (FA) resistance amongst Staphylococcus aureus in New Zealand (NZ) is amongst the highest reported globally, with a recent study describing a resistance rate of approximately 28%. Three FA-resistant S. aureus clones (ST5 MRSA, ST1 MSSA and ST1 MRSA) have emerged over the past decade and now predominate in NZ, and in al...

Objectives: We aimed to examine the dynamics of Staphylococcus aureus nasal carriage in healthy adults. Method: Selected S. aureus strains isolated from weekly nasal swabs obtained from 122 healthy young adults over a 13 week period were spa typed. Results: The median duration of intermittent carriage was 4 weeks (IQR 2-6) and the median inter...

To describe colonisation patterns of Staphylococcus aureus (S. aureus) and Streptococcus pyogenes (S. pyogenes) among pre-school children in New Zealand. Anterior nasal, oropharyngeal, and antecubital fossa swabs were collected from a diverse sample of 139 New Zealand children aged 4 years. Swabs were cultured for S. aureus and S. pyogenes. S. aure...

Our aim was to assess national prescribing trends and determine longitudinal resistance patterns for topical antimicrobials in New Zealand. We observed a dramatic increase in fusidic acid (FA) resistance, and clonal expansion of FA-resistant Staphylococcus aureus. This increase was concurrent with a significant national increase in topical FA dispe...

The genetic structure of Staphylococcus aureus populations sampled from diverse regions of the globe have been the subject of numerous investigations. Here we describe the structure of S. aureus populations collected from the Southwest Pacific. Multi-locus sequence typing was performed on 467 isolates obtained from people with nasal colonization or...

The incidence rate for invasive and noninvasive Staphylococcus aureus infections in New Zealand is among the highest reported in the developed world. Using nationally collated hospital discharge data, we analyzed the epidemiology of serious S. aureus infections in New Zealand during 2000-2011. During this period, incidence of S. aureus skin and sof...

Background We performed a prospective audit of screening for asymptomatic sexually transmissible infections (STIs), during an intensive effort to screen all patients at our hospital-based HIV clinic. We aimed to measure the effectiveness and resource implications of our screening program. Methods: All outpatients who attended during an 8-month peri...

SUMMARY Our aim was to describe the epidemiology and incidence of community-onset invasive S. aureus disease in children presenting to our hospital, and to compare the clonal complexes and virulence genes of S. aureus strains causing invasive and non-invasive disease. The virulence gene repertoire of invasive disease isolates was characterized usin...

Host recognition is the crucial first step in infectious disease pathogenesis. Recognition allows pathogenic bacteria to identify suitable niches and deploy appropriate phenotypes for successful colonization and immune evasion. However, the mechanisms underlying host recognition remain largely unknown. Mounting evidence suggests that urocanate-an i...

New Zealand has a higher incidence of Staphylococcus aureus disease than other developed countries, with significant sociodemographic variation in incidence rates. In contrast to North America, the majority of disease is due to methicillin-susceptible S. aureus (MSSA), although relatively little is known about the comparative demographics of MSSA a...

Background: In the 1970s, there were 2 reports of a late-onset adverse reaction during bolus infusions of benzyl penicillin, characterized by short-lived symptoms, most commonly abdominal pain. The mechanism is not known. We set out to further characterize this reaction. Methods: We conducted a prospective observational study of all adult patien...

More effective antibiotics and a protective vaccine are desperately needed to combat the 'superbug' Staphylococcus aureus. While in vivo pathogenicity studies routinely involve infection of mice with human S. aureus isolates, recent genetic studies have demonstrated that S. aureus lineages are largely host-specific. The use of such animal-adapted S...

S. aureus JSNZ can be easily genetically modified by phage transduction and electroporation. aA lux-encoding plasmid from S. aureus SA113 was transduced into various S. aureus strains using a Φ11 lysate. Results are given as median number of transductants with range for four technical replicates. bA RN4220-derived plasmid was electroporated into va...

Complete DNA microarray results for JSNZ and human CC88 isolates. (XLSX)

The predominant community-associated MRSA strains vary between geographic settings, with ST8-IV USA300 being the commonest clone in North America, and the ST30-IV Southwest Pacific clone established as the dominant clone in New Zealand for the past two decades. Moreover, distinct epidemiological risk factors have been described for colonisation and...

We analysed all cases of community-onset Staphylococcus aureus skin and soft tissue infection in children presenting to our hospital between 2007 and 2010. A total of 1860 children were included. There was significant sociodemographic disparity, with the incidence disproportionately higher in Māori and Pacific Island childrenresiding in deprived ar...

We investigated the population structure of Staphylococcus aureus clonal complex CC121 by mutation discovery at 115 genetic housekeeping loci from each of 154 isolates, sampled on five continents between 1953 and 2009. In addition, we pyro-sequenced the genomes from ten representative isolates. The genome-wide SNPs that were ascertained revealed th...

Polymorphisms discovered in the genome fragments from 154 isolates. (XLS)

Predicted ORFs in ST121 Phage. (XLSX)

Bacterial isolates. (XLS)

Distribution of homoplasious spa-types. Maximum likelihood phylogenetic tree based on 304 SNPs from a selection of housekeeping genes annotated with the respective spa-types. (PDF)

Prophage ΦSaCC121. Prophage modules are color coded: lysogeny, red; DNA replication, orange; transcriptional regulation, yellow; DNA packaging and head, green; tail, blue; lysis, magenta; hypothetical proteins, black. Selected genes are indicated: int, integrase; rep, repressor; p.rep*, putative repressor HTH protein; ant, antirepressor; hel, helic...

Genetic loci and PCR primers used for WAVE analysis. (XLS)

Results of Bayesian tip-association significance testing. (XLSX)

Genome content. (XLSX)

Mutations defining clades within CC121. (XLSX)

Distribution of the six major spa-types. Maximum likelihood phylogenetic tree based on 304 SNPs from a selection of housekeeping genes annotated with the respective spa-types, indicated by the following colors: red, t159; light blue, t284; green, t314; yellow, t435; blue, t645; magenta, t940. (PDF)

PCR primers. (XLS)

PVL nucleotide variation. (XLS)

Pseudomonas aeruginosa is an opportunistic pathogen and an important cause of infection, particularly amongst cystic fibrosis (CF) patients. While specific strains capable of patient-to-patient transmission are known, many infections appear to be caused by unique and unrelated strains. There is a need to understand the relationship between strains...

Map (1∶272,536) of the Logan River showing land use categories. (TIF)

List of the sources, sampling details, relevant epidemiological, clinical and geographical characteristics, multilocus sequence typing data and results of eBURST analyses for the 501 Pseudomonas aeruginosa isolates. (XLSX)

Map (1∶136,268) of the North Pine River showing land use categories. (TIF)

Results of eBURST analysis for the 499 Pseudomonas aeruginosa isolates. Total no. of isolates = 499; Total no. of ST = 272; No. of loci per isolate = 7; No. of identical loci for group definition = 6; Total no. of BURST groups detected = 31; No. of re-samplings for bootstrapping = 1000. (PDF)

Results of eBURST analysis for the 1070 Pseudomonas aeruginosa sequence types listed in the Pseudomonas aeruginosa PubMLST database. P. aeruginosa MLST database: http://pubmlst.org/paeruginosa/; Accessed 04 October 2011; Total no. of STs = 1070; No. of loci per isolate = 7; No. of identical loci for BURST group definition = 6; Total no. of BURST gr...

Little is known about the epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) in most Pacific Island nations. Relatively high rates of MRSA have been reported in Polynesian people living outside the Pacific Islands. To determine the prevalence and characteristics of MRSA, we assessed wound swabs from 399 persons with skin and soft ti...

To estimate the burden of skin and soft tissue infection caused by Staphylococcus aureus (S. aureus), and to determine the effects of ethnicity and age on the rate of skin and soft tissue due to MRSA in the Auckland community. We reviewed the culture and susceptibility results of all wound swabs processed by Auckland's only community microbiology l...

Studies have reported higher rates of diseases caused by Staphylococcus aureus (S. aureus) amongst Maori and Pacific people, compared with people of other ethnicities. We aimed to estimate the prevalence of nasal carriage and to explore demographic differences between S. aureus carriers and non-carriers in Auckland, New Zealand. Nasal swab specimen...

Panton-Valentine leukocidin (PVL) has been linked to invasive community-acquired methicillin-resistant Staphylococcus aureus infections. However, the association between disease and PVL-positive methicillin-susceptible Staphylococcus aureus (MSSA) has not been widely reported. We aimed to examine the epidemiology of PVL in clinical MSSA isolates fr...

We prospectively compared the incidence of ventriculitis associated with external ventricular drains (EVD) impregnated with clindamycin and rifampicin with historical controls. We found the use of antibiotic impregnated (AI) EVDs showed a significant decrease in positive cerebrospinal fluid cultures and a significant delay in time to EVD infection.

Introduction: Staphylococcus aureus [SA] is a common cause of disease in New Zealand, in particular the incidence of SA bacteraemia [SAB] is high. SAB is more common in Māori and Pacific people than people of other ethnicities, but the reasons for this discrepancy are not known. Aim: This thesis investigated a range of reasons for ethnic variation...

Ezetimibe is a cholesterol-lowering agent that modulates intestinal absorption of sterols. It is well tolerated but hepatic toxicity has been reported when ezetimibe is used in conjunction with a statin medication. In this case report, we report severe isolated hyperbilirubinaemia occurring in a patient with occult cirrhosis, probably owing to nona...

A retrospective review was conducted of patients with external ventricular drains (EVDs) in situ in order to ascertain the utility of daily cerebrospinal fluid (CSF) analysis in such patients. All laboratory requests for CSF analysis, which were sent to the Microbiology Department, Auckland City Hospital, New Zealand, were reviewed to identify pati...

It was hypothesised that the time to detect Mycobacterium tuberculosis in liquid culture of sputum from patients with pulmonary tuberculosis may be a better indicator for the duration of respiratory isolation than sputum smear status. Pre-treatment and during-treatment sputum acid-fast bacilli (AFB) smear and culture results were reviewed in 284 pa...

In this paper, we aimed to evaluate the efficacy of flucloxacillin treatment of meningitis caused by methicillin-sensitive Staphylococcus aureus. We identified 33 patients with meningitis due to S. aureus; eight had community-acquired meningitis and 25 had neurosurgical meningitis. Six of the eight patients with community-acquired meningitis were c...

In November 2005 a point prevalence survey of all inpatients at Auckland City Hospital was conducted to define the utilisation of intravascular and urinary devices; to measure the prevalence of infectious complications from these devices; and to provide quality assurance information about the use of these devices. All 830 inpatients admitted on a s...

International guidelines recommend routine microbiological assessment of patients with febrile neutropenia, but do not recommend a change from broad-spectrum antibiotic therapy to pathogen-specific therapy when a clinically relevant organism has been isolated. The aim of the study was to determine the aetiology of febrile neutropenia in adult haema...

Problem: Antibiotic prophylaxis has been shown to reduce the number of postoperative infections following surgery for hip fracture. At Auckland Hospital the policy for antibiotic prophylaxis for hip fracture surgery is for the patient to receive the first dose of antibiotic at the induction of anaesthesia followed by two more doses at 8 hour interv...

Antibiotic prophylaxis has been shown to reduce the number of postoperative infections following surgery for hip fracture. At Auckland Hospital the policy for antibiotic prophylaxis for hip fracture surgery is for the patient to receive the first dose of antibiotic at the induction of anaesthesia followed by two more doses at 8 hour intervals. A pr...