Massey Research Online - Browsing by Author "Fayaz A"

Browsing by Author "Fayaz A"

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Carriage 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, 24/11/2020) 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 SA
Extended-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.
Community health and human-animal contacts on the edges of Bwindi Impenetrable National Park, Uganda
(PLOS, 2021-11-24) Muylaert RL; Davidson B; Ngabirano A; Kalema-Zikusoka G; MacGregor H; Lloyd-Smith JO; Fayaz A; Knox MA; Hayman DTS; Fèvre E
Cross-species transmission of pathogens is intimately linked to human and environmental health. With limited healthcare and challenging living conditions, people living in poverty may be particularly susceptible to endemic and emerging diseases. Similarly, wildlife is impacted by human influences, including pathogen sharing, especially for species in close contact with people and domesticated animals. Here we investigate human and animal contacts and human health in a community living around the Bwindi Impenetrable National Park (BINP), Uganda. We used contact and health survey data to identify opportunities for cross-species pathogen transmission, focusing mostly on people and the endangered mountain gorilla. We conducted a survey with background questions and self-reported diaries to investigate 100 participants' health, such as symptoms and behaviours, and contact patterns, including direct contacts and sightings over a week. Contacts were revealed through networks, including humans, domestic, peri-domestic, and wild animal groups for 1) contacts seen in the week of background questionnaire completion, and 2) contacts seen during the diary week. Participants frequently felt unwell during the study, reporting from one to 10 disease symptoms at different intensity levels, with severe symptoms comprising 6.4% of the diary records and tiredness and headaches the most common symptoms. After human-human contacts, direct contact with livestock and peri-domestic animals were the most common. The contact networks were moderately connected and revealed a preference in contacts within the same taxon and within their taxa groups. Sightings of wildlife were much more common than touching. However, despite contact with wildlife being the rarest of all contact types, one direct contact with a gorilla with a timeline including concerning participant health symptoms was reported. When considering all interaction types, gorillas mostly exhibited intra-species contact, but were found to interact with five other species, including people and domestic animals. Our findings reveal a local human population with recurrent symptoms of illness in a location with intense exposure to factors that can increase pathogen transmission, such as direct contact with domestic and wild animals and proximity among animal species. Despite significant biases and study limitations, the information generated here can guide future studies, such as models for disease spread and One Health interventions.
Community health and human-animal contacts on the edges of Bwindi Impenetrable National Park, Uganda (preprint)
(2021-07-23) Muylaert RL; Davidson B; Ngabirano A; Kalema-Zikusoka G; MacGregor H; Lloyd-Smith JO; Fayaz A; Knox MA; Hayman DTS
Genomic adaptations of Campylobacter jejuni to long-term human colonization
(BioMed Central Ltd, 2021-12-10) Bloomfield SJ; Midwinter AC; Biggs PJ; French NP; Marshall JC; Hayman DTS; Carter PE; Mather AE; Fayaz A; Thornley C; Kelly DJ; Benschop J
BACKGROUND: Campylobacter is a genus of bacteria that has been isolated from the gastrointestinal tract of humans and animals, and the environments they inhabit around the world. Campylobacter adapt to new environments by changes in their gene content and expression, but little is known about how they adapt to long-term human colonization. In this study, the genomes of 31 isolates from a New Zealand patient and 22 isolates from a United Kingdom patient belonging to Campylobacter jejuni sequence type 45 (ST45) were compared with 209 ST45 genomes from other sources to identify the mechanisms by which Campylobacter adapts to long-term human colonization. In addition, the New Zealand patient had their microbiota investigated using 16S rRNA metabarcoding, and their level of inflammation and immunosuppression analyzed using biochemical tests, to determine how Campylobacter adapts to a changing gastrointestinal tract. RESULTS: There was some evidence that long-term colonization led to genome degradation, but more evidence that Campylobacter adapted through the accumulation of non-synonymous single nucleotide polymorphisms (SNPs) and frameshifts in genes involved in cell motility, signal transduction and the major outer membrane protein (MOMP). The New Zealand patient also displayed considerable variation in their microbiome, inflammation and immunosuppression over five months, and the Campylobacter collected from this patient could be divided into two subpopulations, the proportion of which correlated with the amount of gastrointestinal inflammation. CONCLUSIONS: This study demonstrates how genomics, phylogenetics, 16S rRNA metabarcoding and biochemical markers can provide insight into how Campylobacter adapts to changing environments within human hosts. This study also demonstrates that long-term human colonization selects for changes in Campylobacter genes involved in cell motility, signal transduction and the MOMP; and that genetically distinct subpopulations of Campylobacter evolve to adapt to the changing gastrointestinal environment.
Population Structure and Antimicrobial Resistance in Campylobacter jejuni and C. coli Isolated from Humans with Diarrhea and from Poultry, East Africa.
(Centers for Disease Control and Prevention, 2024-10) French NP; Thomas KM; Amani NB; Benschop J; Bigogo GM; Cleaveland S; Fayaz A; Hugho EA; Karimuribo ED; Kasagama E; Maganga R; Melubo ML; Midwinter AC; Mmbaga BT; Mosha VV; Mshana FI; Munyua P; Ochieng JB; Rogers L; Sindiyo E; Swai ES; Verani JR; Widdowson M-A; Wilkinson DA; Kazwala RR; Crump JA; Zadoks RN
Campylobacteriosis and antimicrobial resistance (AMR) are global public health concerns. Africa is estimated to have the world's highest incidence of campylobacteriosis and a relatively high prevalence of AMR in Campylobacter spp. from humans and animals. Few studies have compared Campylobacter spp. isolated from humans and poultry in Africa using whole-genome sequencing and antimicrobial susceptibility testing. We explored the population structure and AMR of 178 Campylobacter isolates from East Africa, 81 from patients with diarrhea in Kenya and 97 from 56 poultry samples in Tanzania, collected during 2006-2017. Sequence type diversity was high in both poultry and human isolates, with some sequence types in common. The estimated prevalence of multidrug resistance, defined as resistance to >3 antimicrobial classes, was higher in poultry isolates (40.9%, 95% credible interval 23.6%-59.4%) than in human isolates (2.5%, 95% credible interval 0.3%-6.8%), underlining the importance of antimicrobial stewardship in livestock systems.
The characterisation of antimicrobial resistant Escherichia coli from dairy calves.
(Microbiology Society, 2023-08) Mwenifumbo M; Cookson AL; Zhao S; Fayaz A; Browne AS; Benschop J; Burgess SA
Introduction. Dairy calves, particularly pre-weaned calves have been identified as a common source of multidrug resistant (MDR) Escherichia coli. Gap statement. E. coli strains isolated from dairy calves and the location of their resistance genes (plasmid or chromosomal) have not been well characterised. Aim. To characterise the phenotypic and genotypic features as well as the population structure of antimicrobial-resistant E. coli isolated from calves located on dairy farms that feed waste-milk to their replacement calves. Methodology. Recto-anal swab enrichments from 40 dairy calves (≤ 14 days old) located on four dairy farms were examined for tetracycline, streptomycin, ciprofloxacin, and third-generation cephalosporin resistant E. coli. Whole genome sequencing was performed using both short- and long-read technologies on selected antimicrobial resistant E. coli. Results. Fifty-eight percent (23/40) of calves harboured antimicrobial resistant E. coli: 43 % (17/40) harboured tetracycline resistant, and 23 % (9/40) harboured chromosomal mediated AmpC producing E. coli. Whole genome sequencing of 27 isolates revealed five sequence types, with ST88 being the dominant ST (17/27, 63 % of the sequenced isolates) followed by ST1308 (3/27, 11 %), along with the extraintestinal pathogenic E. coli lineages ST69 (3/27, 11 %), ST10 (2/27, 7 %), and ST58 (2/27, 7 %). Additionally, 16 isolates were MDR, harbouring additional resistance genes that were not tested phenotypically. Oxford Nanopore long-read sequencing technologies enabled the location of multiple resistant gene cassettes in IncF plasmids to be determined. Conclusion. Our study identified a high incidence of tetracycline and streptomycin-resistant E. coli in dairy calves, and highlighted the presence of multidrug-resistant strains, emphasising the need for further investigation into potential associations with farm management practices.
Transmission dynamics of an antimicrobial resistant Campylobacter jejuni lineage in New Zealand’s commercial poultry network
(Elsevier B.V, 2021-12) Greening SS; Zhang J; Midwinter AC; Wilkinson DA; Fayaz A; Williamson DA; Anderson MJ; Gates MC; French NP
Understanding the relative contribution of different between-farm transmission pathways is essential in guiding recommendations for mitigating disease spread. This study investigated the association between contact pathways linking poultry farms in New Zealand and the genetic relatedness of antimicrobial resistant Campylobacter jejuni Sequence Type 6964 (ST-6964), with the aim of identifying the most likely contact pathways that contributed to its rapid spread across the industry. Whole-genome sequencing was performed on 167C. jejuni ST-6964 isolates sampled from across 30 New Zealand commercial poultry enterprises. The genetic relatedness between isolates was determined using whole genome multilocus sequence typing (wgMLST). Permutational multivariate analysis of variance and distance-based linear models were used to explore the strength of the relationship between pairwise genetic associations among the C. jejuni isolates and each of several pairwise distance matrices, indicating either the geographical distance between farms or the network distance of transportation vehicles. Overall, a significant association was found between the pairwise genetic relatedness of the C. jejuni isolates and the parent company, the road distance and the network distance of transporting feed vehicles. This result suggests that the transportation of feed within the commercial poultry industry as well as other local contacts between flocks, such as the movements of personnel, may have played a significant role in the spread of C. jejuni. However, further information on the historical contact patterns between farms is needed to fully characterise the risk of these pathways and to understand how they could be targeted to reduce the spread of C. jejuni.
Updating the genomic taxonomy and epidemiology of Campylobacter hyointestinalis
(Springer Nature Limited, 2018-02-05) Wilkinson DA; O'Donnell AJ; Akhter RN; Fayaz A; Mack HJ; Rogers LE; Biggs PJ; French NP; Midwinter AC
Campylobacter hyointestinalis is a member of an emerging group of zoonotic Campylobacter spp. that are increasingly identified in both gastric and non-gastric disease in humans. Here, we discovered C. hyointestinalis in three separate classes of New Zealand ruminant livestock; cattle, sheep and deer. To investigate the relevance of these findings we performed a systematic literature review on global C. hyointestinalis epidemiology and used comparative genomics to better understand and classify members of the species. We found that C. hyointestinalis subspecies hyointestinalis has an open pangenome, with accessory gene contents involved in many essential processes such as metabolism, virulence and defence. We observed that horizontal gene transfer is likely to have played an overwhelming role in species diversification, favouring a public-goods-like mechanism of gene ‘acquisition and resampling’ over a tree-of-life-like vertical inheritance model of evolution. As a result, simplistic gene-based inferences of taxonomy by similarity are likely to be misleading. Such genomic plasticity will also mean that local evolutionary histories likely influence key species characteristics, such as host-association and virulence. This may help explain geographical differences in reported C. hyointestinalis epidemiology and limits what characteristics may be generalised, requiring further genomic studies of C. hyointestinalis in areas where it causes disease.
"We don't really do doctors." messages from people diagnosed with occupational leptospirosis for medical professionals on infection, hospitalisation, and long-term effects.
(Elsevier B.V., 2023-09) Prinsen G; Baker M; Benschop J; Collins-Emerson J; Douwes J; Fayaz A; Littlejohn S; Nisa S; Quin T; Yeung P
Leptospirosis is largely an occupational disease for people working with livestock in Aotearoa New Zealand. Introduction of livestock vaccination and use of personal protective equipment has been associated with a reduction in the incidence. However, the incidence of occupational leptospirosis remains high, with significant burdens for affected families and healthcare system. For this article, a subset of thirteen participants from a nationwide leptospirosis case-control study (2019-2021) who were diagnosed with leptospirosis and worked with livestock at the time of illness were invited and agreed to a semi-structured interview. Interviewees reflected on their experiences as messages for medical professionals. The analysis of transcripts reveals widely shared experiences with infection, hospitalisation, and treatment, as well as long-term effects and recovery. Conclusions for medical professionals include that ill workers continue to have their diagnosis of leptospirosis delayed. This delay may contribute to more than half the people ill with leptospirosis hospitalised. Further, medical professionals' communication and relationship with ill people strongly colours the latter's experience, for good or for bad. Moreover, most interviewees experienced a recovery process that took several months of feeling tired, which undermined professional performance and emotional wellbeing.

Browsing by Author "Fayaz A"

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