Browsing by Author "Marshall JC"
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- ItemCarriage of Extended-Spectrum-Beta-Lactamase- and AmpC Beta-Lactamase-Producing Escherichia coli Strains from Humans and Pets in the Same Households.(American Society for Microbiology, 2020-11-24) Toombs-Ruane LJ; Benschop J; French NP; Biggs PJ; Midwinter AC; Marshall JC; Chan M; Drinković D; Fayaz A; Baker MG; Douwes J; Roberts MG; Burgess SAExtended-spectrum-beta-lactamase (ESBL)- or AmpC beta-lactamase (ACBL)-producing Escherichia coli bacteria are the most common cause of community-acquired multidrug-resistant urinary tract infections (UTIs) in New Zealand. The carriage of antimicrobial-resistant bacteria has been found in both people and pets from the same household; thus, the home environment may be a place where antimicrobial-resistant bacteria are shared between humans and pets. In this study, we sought to determine whether members (pets and people) of the households of human index cases with a UTI caused by an ESBL- or ACBL-producing E. coli strain also carried an ESBL- or ACBL-producing Enterobacteriaceae strain and, if so, whether it was a clonal match to the index case clinical strain. Index cases with a community-acquired UTI were recruited based on antimicrobial susceptibility testing of urine isolates. Fecal samples were collected from 18 non-index case people and 36 pets across 27 households. Eleven of the 27 households screened had non-index case household members (8/18 people and 5/36 animals) positive for ESBL- and/or ACBL-producing E. coli strains. Whole-genome sequence analysis of 125 E. coli isolates (including the clinical urine isolates) from these 11 households showed that within seven households, the same strain of ESBL-/ACBL-producing E. coli was cultured from both the index case and another person (5/11 households) or pet dog (2/11 households). These results suggest that transmission within the household may contribute to the community spread of ESBL- or ACBL-producing E. coliIMPORTANCEEnterobacteriaceae that produce extended-spectrum beta-lactamases (ESBLs) and AmpC beta-lactamases (ACBLs) are important pathogens and can cause community-acquired illnesses, such as urinary tract infections (UTIs). Fecal carriage of these resistant bacteria by companion animals may pose a risk for transmission to humans. Our work evaluated the sharing of ESBL- and ACBL-producing E. coli isolates between humans and companion animals. We found that in some households, dogs carried the same strain of ESBL-producing E. coli as the household member with a UTI. This suggests that transmission events between humans and animals (or vice versa) are likely occurring within the home environment and, therefore, the community as a whole. This is significant from a health perspective, when considering measures to minimize community transmission, and highlights that in order to manage community spread, we need to consider interventions at the household level.
- ItemCulture independent analysis using gnd as a target gene to assess Escherichia coli diversity and community structure.(2017-04-12) Cookson AL; Biggs PJ; Marshall JC; Reynolds A; Collis RM; French NP; Brightwell GCurrent culture methods to investigate changes in Escherichia coli community structure are often slow and laborious. Genes such as gnd (6-phosphogluconate dehydrogenase) have a highly variable nucleotide sequence and may provide a target for E. coli microbiome analysis using culture-independent methods. Metabarcoded PCR primers were used to generate separate libraries from calf faecal samples for high throughput sequencing. Although a total of 348 separate gnd sequence types (gSTs) were identified, 188 were likely to be due to sequencing errors. Of the remaining 160 gSTs, 92 did not match those in a database of 319 separate gnd sequences. 'Animal' was the main determinant of E. coli diversity with limited impact of sample type or DNA extraction method on intra-host E. coli community variation from faeces and recto-anal mucosal swab samples. This culture-independent study has addressed the difficulties of quantifying bacterial intra-species diversity and revealed that, whilst individual animals may harbour >50 separate E. coli strains, communities are dominated by <10 strains alongside a large pool of subdominant strains present at low abundances. This method will be useful for characterising the diversity and population structure of E. coli in experimental studies designed to assess the impact of interventions on the gut microbiome.
- ItemExpression of Renal Vitamin D and Phosphatonin-Related Genes in a Sheep Model of Osteoporosis(MDPI (Basel, Switzerland), 2022-01) Dittmer KE; Chernyavtseva A; Marshall JC; Cabrera D; Wolber FM; Kruger M; Bienko M; Radzki RPOsteoporosis is a significant public health issue around the world, with post-menopausal osteoporosis due to estrogen deficiency resulting in approximately ¾ of cases. In this study, 18 aged Merino ewes were ovariectomized, and 10 were controls. Three of the ovariectomized ewes were treated weekly with 400 mg of methylprednisolone for 5 months and three were treated weekly for 2 months, followed by a 3-month recovery period. At 2 months, five control animals and six ovariectomized animals were euthanized. At 5 months, all the remaining ewes were euthanized. Kidney samples were collected postmortem for qPCR analysis of NPT1, PTH1R, NPT2a, NPT2c, Klotho, FGFR1IIIc, VDR, CYP24A1, CYP27B1, TRPV5, TRPV6, CalD9k, CalD28k, PMCA and NCX1. Ovariectomized sheep had significantly greater VDR expression compared with other groups. Ovariectomized sheep treated with glucocorticoids for 2 months followed by euthanasia at 5 months showed significant differences in TRPV5, CYP24A1 and klotho gene expression compared to other groups. Differences in klotho expression were most marked after adjustment for repeated measures (p = 0.1). Klotho is known as the "anti-aging" hormone and is involved in calcium and phosphorus metabolism. Klotho may be involved in the recovery of bone mineral density in ovariectomized sheep treated with glucocorticoids for 2 months followed by euthanasia at 5 months. Further research on the role of klotho is recommended.
- ItemExtended-spectrum β-lactamase- and AmpC β-lactamase-producing Enterobacterales associated with urinary tract infections in the New Zealand community: a case-control study(Elsevier Ltd on behalf of International Society for Infectious Diseases, 2023-03) Toombs-Ruane LJ; Marshall JC; Benschop J; Drinković D; Midwinter AC; Biggs PJ; Grange Z; Baker MG; Douwes J; Roberts MG; French NP; Burgess SAOBJECTIVES: To assess whether having a pet in the home is a risk factor for community-acquired urinary tract infections associated with extended-spectrum β-lactamase (ESBL)- or AmpC β-lactamase (ACBL)- producing Enterobacterales. METHODS: An unmatched case-control study was conducted between August 2015 and September 2017. Cases (n = 141) were people with community-acquired urinary tract infection (UTI) caused by ESBL- or ACBL-producing Enterobacterales. Controls (n = 525) were recruited from the community. A telephone questionnaire on pet ownership and other factors was administered, and associations were assessed using logistic regression. RESULTS: Pet ownership was not associated with ESBL- or ACBL-producing Enterobacterales-related human UTIs. A positive association was observed for recent antimicrobial treatment, travel to Asia in the previous year, and a doctor's visit in the last 6 months. Among isolates with an ESBL-/ACBL-producing phenotype, 126/134 (94%) were Escherichia coli, with sequence type 131 being the most common (47/126). CONCLUSIONS: Companion animals in the home were not found to be associated with ESBL- or ACBL-producing Enterobacterales-related community-acquired UTIs in New Zealand. Risk factors included overseas travel, recent antibiotic use, and doctor visits.
- ItemGenomic Analysis of Salmonella enterica Serovar Typhimurium DT160 Associated with a 14-Year Outbreak, New Zealand, 1998-2012.(2017-06) Bloomfield SJ; Benschop J; Biggs PJ; Marshall JC; Hayman DTS; Carter PE; Midwinter AC; Mather AE; French NPDuring 1998-2012, an extended outbreak of Salmonella enterica serovar Typhimurium definitive type 160 (DT160) affected >3,000 humans and killed wild birds in New Zealand. However, the relationship between DT160 within these 2 host groups and the origin of the outbreak are unknown. Whole-genome sequencing was used to compare 109 Salmonella Typhimurium DT160 isolates from sources throughout New Zealand. We provide evidence that DT160 was introduced into New Zealand around 1997 and rapidly propagated throughout the country, becoming more genetically diverse over time. The genetic heterogeneity was evenly distributed across multiple predicted functional protein groups, and we found no evidence of host group differentiation between isolates collected from human, poultry, bovid, and wild bird sources, indicating ongoing transmission between these host groups. Our findings demonstrate how a comparative genomic approach can be used to gain insight into outbreaks, disease transmission, and the evolution of a multihost pathogen after a probable point-source introduction.
- ItemLost in the Forest(Cold Spring Harbor Laboratory, 2022) Smith HL; Biggs PJ; French NP; Smith ANH; Marshall JCTo date, there remains no satisfactory solution for absent levels in random forest models. Absent levels are levels of a predictor variable encountered during prediction for which no explicit rule exists. Imposing an order on nominal predictors allows absent levels to be integrated and used for prediction. The ordering of predictors has traditionally been via class probabilities with absent levels designated the lowest order. Using a combination of simulated data and pathogen source-attribution models using whole-genome sequencing data, we examine how the method of ordering predictors with absent levels can (i) systematically bias a model, and (ii) affect the out-of-bag error rate. We show that the traditional approach is systematically biased and underestimates out-of-bag error rates, and that this bias is resolved by ordering absent levels according to the a priori hypothesis of equal class probability. We present a novel method of ordering predictors via principal coordinates analysis (PCO) which capitalizes on the similarity between pairs of predictor levels. Absent levels are designated an order according to their similarity to each of the other levels in the training data. We show that the PCO method performs at least as well as the traditional approach of ordering and is not biased.
- ItemRisk Factors for Hospitalisation amongst Leptospirosis Patients in New Zealand(MDPI (Basel, Switzerland), 2021-12) Sokolova M; Marshall JC; Benschop J; Frean JLeptospirosis is a neglected zoonotic disease that is widespread in tropical and subtropical regions such as Oceania, which includes New Zealand. The incidence rate of leptospirosis in New Zealand remains high in comparison to other high-income countries, with over half of the notified patients hospitalised, and the factors associated with hospitalisation are poorly understood. This study aimed to estimate the risk factors for hospitalisation amongst leptospirosis patients using passive surveillance data: notifications from 1 January 1999 to 31 December 2017 extracted from New Zealand's notifiable disease database. There were 771 hospitalised and 673 non-hospitalised patients. Multivariable logistic regression was used to identify risk factors. The year of notification was significantly and positively associated with hospitalisation, with adjusted (adj.) OR 1.03 (95% CI:1.01-1.05). Occupation was significantly associated with hospitalisation, with the adjusted odds of hospitalisation amongst dairy farmers notified with leptospirosis at adj. OR 1.44 (95% CI: 1.02-2.02) times the adjusted odds of hospitalisation amongst farmers that worked with other livestock. Seropositivity for Leptospira interrogans Copenhageni (adj. OR 5.96, 95% CI: 1.68-21.17) and Pomona (adj. OR 1.14, 95% CI: 0.74-1.74)) was more likely to result in hospitalisation when compared to Leptospira borgpetersenii Ballum (baseline). Seropositivity for Leptospira borgpetersenii Hardjo (adj. OR 0.71, 95% CI: 0.49-1.01) and Tarassovi (adj. OR 0.39, 95% CI: 0.23-0.66) was less likely to result in hospitalisation when compared to Ballum (baseline). All the estimates were additionally adjusted for the effect of sex, age, ethnicity, reported occupational exposure, geographical location, reported season, and deprivation status Although passive surveillance data has limitations we have been able to identify that the New Zealand dairy farming population may benefit from a targeted awareness campaign.
- ItemTransmission Dynamics of Shiga Toxin-Producing Escherichia coli in New Zealand Cattle from Farm to Slaughter.(American Society for Microbiology, 2021-05-11) Browne AS; Midwinter AC; Withers H; Cookson AL; Biggs PJ; Marshall JC; Benschop J; Hathaway S; Rogers L; Nisa S; Hranac CR; Winkleman T; French NPCattle are asymptomatic carriers of Shiga toxin-producing Escherichiacoli (STEC) strains that can cause serious illness or death in humans. In New Zealand, contact with cattle feces and living near cattle populations are known risk factors for human STEC infection. Contamination of fresh meat with STEC strains also leads to the potential for rejection of consignments by importing countries. We used a combination of PCR/matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF) and whole-genome sequencing (WGS) to evaluate the presence and transmission of STEC on farms and in processing plants to better understand the potential pathways for human exposure and thus mitigate risk. Animal and environmental samples (n = 2,580) were collected from six farms and three meat processing plants in New Zealand during multiple sampling sessions in spring of 2015 and 2016. PCR/MALDI-TOF analysis revealed that 6.2% were positive for "Top 7" STEC. Top 7 STEC strains were identified in all sample sources (n = 17) tested. A marked increase in Top 7 STEC prevalence was observed between calf hides on farm (6.3% prevalence) and calf hides at processing plants (25.1% prevalence). Whole-genome sequencing was performed on Top 7 STEC bacterial isolates (n = 40). Analysis of STEC O26 (n = 25 isolates) revealed relatively low genetic diversity on individual farms, consistent with the presence of a resident strain disseminated within the farm environment. Public health efforts should focus on minimizing human contact with fecal material on farms and during handling, transport, and slaughter of calves. Meat processing plants should focus on minimizing cross-contamination between the hides of calves in a cohort during transport, lairage, and slaughter. IMPORTANCE Cattle are asymptomatic carriers of Shiga toxin-producing E. coli (STEC) strains, which can cause serious illness or death in humans. Contact with cattle feces and living near cattle are known risk factors for human STEC infection. This study evaluated STEC carriage in young calves and the farm environment with an in-depth evaluation of six farms and three meat processing plants over 2 years. An advanced molecular detection method and whole-genome sequencing were used to provide a detailed evaluation of the transmission of STEC both within and between farms. The study revealed widespread STEC contamination within the farm environment, but no evidence of recent spread between farms. Contamination of young dairy calf hides increased following transport and holding at meat processing plants. The elimination of STEC in farm environments may be very difficult given the multiple transmission routes; interventions should be targeted at decreasing fecal contamination of calf hides during transport, lairage, and processing.