Journal Articles
Permanent URI for this collectionhttps://mro.massey.ac.nz/handle/10179/7915
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Item Mutations in the riboflavin biosynthesis pathway confer resistance to furazolidone and abolish the synergistic interaction between furazolidone and vancomycin in Escherichia coli.(Microbiology Society, England, 2025-02-11) Wykes H; Le VVH; Rakonjac JThe combined application of furazolidone and vancomycin has previously been shown to be synergistic against Gram-negative pathogens, with great therapeutic promise. However, the emergence and mechanism of resistance to this antibiotic combination have not been characterized. To fill this gap, we here selected Escherichia coli progeny for growth on the furazolidone-vancomycin combination at the concentration where the parent was sensitive. We show that selected clones were associated with increased resistance to neither, only one drug, or both furazolidone and vancomycin, but in all cases were associated with a decrease in the growth inhibition synergy. Using whole-genome sequencing, we identified various gene mutations in the resistant mutants. We further investigated the mechanism behind the most frequently arising mutations, those in the riboflavin biosynthesis genes ribB and ribE, that represent novel mutations causing furazolidone resistance and diminished vancomycin-furazolidone synergy. It was found that these ribB/ribE mutations act predominantly by decreasing the activity of the NfsA and NfsB nitroreductases. The emergence of the ribB/ribE mutations imposes a significant fitness cost on bacterial growth. Surprisingly, supplementing the medium with riboflavin, which compensates for the affected riboflavin biosynthesis pathway, could restore the normal growth of the ribB/ribE mutants while having no effects on the furazolidone resistance phenotype. Searching the ribB/ribE mutations in the public sequencing database detects the presence of the furazolidone-resistance-conferring ribE mutations (TKAG131-134 deletion or duplication) in clinical isolates from different countries. Hypotheses explaining why these ribE mutations were found in clinical isolates despite having poor fitness were further discussed.Item New Campylobacter Lineages in New Zealand Freshwater: Pathogenesis and Public Health Implications(John Wiley and Sons, 2024-12) Cookson AL; Burgess S; Midwinter AC; Marshall JC; Moinet M; Rogers L; Fayaz A; Biggs PJ; Brightwell GThis study investigated the diversity of thermophilic Campylobacter species isolated from three New Zealand freshwater catchments affected by pastoral and urban activities. Utilising matrix-assisted laser desorption ionisation-time of flight and whole genome sequence analysis, the study identified Campylobacter jejuni (n = 46, 46.0%), C. coli (n = 39, 39%), C. lari (n = 4, 4.0%), and two novel Campylobacter species lineages (n = 11, 11%). Core genome sequence analysis provided evidence of prolonged persistence or continuous faecal shedding of closely related strains. The C. jejuni isolates displayed distinct sequence types (STs) associated with human, ruminant, and environmental sources, whereas the C. coli STs included waterborne ST3302 and ST7774. Recombination events affecting loci implicated in human pathogenesis and environmental persistence were observed, particularly in the cdtABC operon (encoding the cytolethal distending toxin) of non-human C. jejuni STs. A low diversity of antimicrobial resistance genes (aadE-Cc in C. coli), with genotype/phenotype concordance for tetracycline resistance (tetO) in three ST177 isolates, was noted. The data suggest the existence of two types of naturalised waterborne Campylobacter: environmentally persistent strains originating from waterbirds and new environmental species not linked to human campylobacteriosis. Identifying and understanding naturalised Campylobacter species is crucial for accurate waterborne public health risk assessments and the effective allocation of resources for water quality management.Item Global Distribution of Invasive Serotype 35D Streptococcus pneumoniae Isolates following Introduction of 13-Valent Pneumococcal Conjugate Vaccine.(American Society for Microbiology, 2018-06-25) Lo SW; Gladstone RA; van Tonder AJ; Hawkins PA; Kwambana-Adams B; Cornick JE; Madhi SA; Nzenze SA; du Plessis M; Kandasamy R; Carter PE; Eser ÖK; Ho PL; Elmdaghri N; Shakoor S; Clarke SC; Antonio M; Everett DB; von Gottberg A; Klugman KP; McGee L; Breiman RF; Bentley SDA newly recognized pneumococcal serotype, 35D, which differs from the 35B polysaccharide in structure and serology by not binding to factor serum 35a, was recently reported. The genetic basis for this distinctive serology is due to the presence of an inactivating mutation in wciG, which encodes an O-acetyltransferase responsible for O-acetylation of a galactofuranose. Here, we assessed the genomic data of a worldwide pneumococcal collection to identify serotype 35D isolates and understand their geographical distribution, genetic background, and invasiveness potential. Of 21,980 pneumococcal isolates, 444 were originally typed as serotype 35B by PneumoCaT. Analysis of the wciG gene revealed 23 isolates from carriage (n = 4) and disease (n = 19) with partial or complete loss-of-function mutations, including mutations resulting in premature stop codons (n = 22) and an in-frame mutation (n = 1). These were selected for further analysis. The putative 35D isolates were geographically widespread, and 65.2% (15/23) of them was recovered after the introduction of pneumococcal conjugate vaccine 13 (PCV13). Compared with serotype 35B isolates, putative serotype 35D isolates have higher invasive disease potentials based on odds ratios (OR) (11.58; 95% confidence interval[CI], 1.42 to 94.19 versus 0.61; 95% CI, 0.40 to 0.92) and a higher prevalence of macrolide resistance mediated by mefA (26.1% versus 7.6%; P = 0.009). Using the Quellung reaction, 50% (10/20) of viable isolates were identified as serotype 35D, 25% (5/20) as serotype 35B, and 25% (5/20) as a mixture of 35B/35D. The discrepancy between phenotype and genotype requires further investigation. These findings illustrated a global distribution of an invasive serotype, 35D, among young children post-PCV13 introduction and underlined the invasive potential conferred by the loss of O-acetylation in the pneumococcal capsule.Item Molecular epidemiology and whole genome sequencing analysis of clinical Mycobacterium bovis from Ghana.(PLOS, 2019-03-04) Otchere ID; van Tonder AJ; Asante-Poku A; Sánchez-Busó L; Coscollá M; Osei-Wusu S; Asare P; Aboagye SY; Ekuban SA; Yahayah AI; Forson A; Baddoo A; Laryea C; Parkhill J; Harris SR; Gagneux S; Yeboah-Manu D; Spigelman MBackground Bovine tuberculosis (bTB) caused by Mycobacterium bovis is a re-emerging problem in both livestock and humans. The association of some M. bovis strains with hyper-virulence, MDR-TB and disseminated disease makes it imperative to understand the biology of the pathogen. Methods Mycobacterium bovis (15) among 1755 M. tuberculosis complex (MTBC) isolated between 2012 and 2014 were characterized and analyzed for associated patient demography and other risk factors. Five of the M. bovis isolates were whole-genome sequenced and comparatively analyzed against a global collection of published M. bovis genomes. Results Mycobacterium bovis was isolated from 3/560(0.5%) females and 12/1195(1.0%) males with pulmonary TB. The average age of M. bovis infected cases was 46.8 years (7-72years). TB patients from the Northern region of Ghana (1.9%;4/212) had a higher rate of infection with M. bovis (OR = 2.7,p = 0.0968) compared to those from the Greater Accra region (0.7%;11/1543). Among TB patients with available HIV status, the odds of isolating M. bovis from HIV patients (2/119) was 3.3 higher relative to non-HIV patients (4/774). Direct contact with livestock or their unpasteurized products was significantly associated with bTB (p<0.0001, OR = 124.4,95% CI = 30.1–508.3). Two (13.3%) of the M. bovis isolates were INH resistant due to the S315T mutation in katG whereas one (6.7%) was RIF resistant with Q432P and I1491S mutations in rpoB. M. bovis from Ghana resolved as mono-phyletic branch among mostly M. bovis from Africa irrespective of the host and were closest to the root of the global M. bovis phylogeny. M. bovis-specific amino acid mutations were detected among MTBC core genes such as mce1A, mmpL1, pks6, phoT, pstB, glgP and Rv2955c. Additional mutations P6T in chaA, G187E in mgtC, T35A in Rv1979c, S387A in narK1, L400F in fas and A563T in eccA1 were restricted to the 5 clinical M. bovis from Ghana. Conclusion Our data indicate potential zoonotic transmission of bTB in Ghana and hence calls for intensified public education on bTB, especially among risk groups..Item 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 RNCampylobacteriosis 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.Item Extensive bacteriocin gene shuffling in the Streptococcus bovis/Streptococcus equinus complex reveals gallocin D with activity against vancomycin resistant enterococci.(Springer Nature Limited, 2020-08-10) Hill D; O'Connor PM; Altermann E; Day L; Hill C; Stanton C; Ross RPStreptococcus gallolyticus LL009 produces gallocin D, a narrow spectrum two component bacteriocin with potent activity against vancomycin-resistant enterococci. Gallocin D is distinct from gallocin A, a separate two component bacteriocin produced by S. gallolyticus. Although the gene clusters encoding gallocin A and gallocin D have a high degree of gene synteny, the structural genes are highly variable and appear to have undergone gene shuffling with other streptococcal species. Gallocin D was analysed in laboratory-based experiments. The mature peptides are 3,343 ± 1 Da and 3,019 ± 1 Da and could be readily synthesized and display activity against a vancomycin resistant Enterococcus strain EC300 with a MIC value of 1.56 µM. Importantly, these bacteriocins could contribute to the ability of S. gallolyticus to colonize the colon where they have been associated with colorectal cancer.Item Development of a cross-sectoral antimicrobial resistance capability assessment framework.(BMJ Publishing Group, 2024-02-05) Ferdinand AS; McEwan C; Lin C; Betham K; Kandan K; Tamolsaian G; Pugeva B; McKenzie J; Browning G; Gilkerson J; Coppo M; James R; Peel T; Levy S; Townell N; Jenney A; Stewardson A; Cameron D; Macintyre A; Buising K; Howden BP; Biswas SAntimicrobial resistance (AMR) is an urgent and growing global health concern, and a clear understanding of existing capacities to address AMR, particularly in low-income and middle-income countries (LMICs), is needed to inform national priorities, investment targets and development activities. Across LMICs, there are limited data regarding existing mechanisms to address AMR, including national AMR policies, current infection prevention and antimicrobial prescribing practices, antimicrobial use in animals, and microbiological testing capacity for AMR. Despite the development of numerous individual tools designed to inform policy formulation and implementation or surveillance interventions to address AMR, there is an unmet need for easy-to-use instruments that together provide a detailed overview of AMR policy, practice and capacity. This paper describes the development of a framework comprising five assessment tools which provide a detailed assessment of country capacity to address AMR within both the human and animal health sectors. The framework is flexible to meet the needs of implementers, as tools can be used separately to assess the capacity of individual institutions or as a whole to align priority-setting and capacity-building with AMR National Action Plans (NAPs) or national policies. Development of the tools was conducted by a multidisciplinary team across three phases: (1) review of existing tools; (2) adaptation of existing tools; and (3) piloting, refinement and finalisation. The framework may be best used by projects which aim to build capacity and foster cross-sectoral collaborations towards the surveillance of AMR, and by LMICs wishing to conduct their own assessments to better understand capacity and capabilities to inform future investments or the implementation of NAPs for AMR.Item Time trends in positive gonorrhoea diagnoses at the Christchurch Sexual Health Service (2012-2022): a data audit study.(CSIRO Publishing, 2024-06-27) Denison HJ; Creighton J; Douwes J; Coshall M; Young H; Tang WBackground Gonorrhoea infections and antimicrobial resistance are rising in many countries, particularly among men who have sex with men, and an increasing proportion of infection is detected at extragenital sites. This study assessed trends in gonorrhoea diagnoses and antibiotic resistance at a sexual health service in New Zealand that followed national guidelines for specimen collection. Methods Routinely-collected data from Canterbury Health Laboratories of specimens taken at the Christchurch Sexual Health Service 2012–2022 were audited. Descriptive results included the number of patient testing events positive for gonorrhoea per year and site of infection (extragenital/urogenital). Annual test-positivity was calculated (number of positive patient testing events divided by total number of testing events) and the Cochran-Armitage Test for Trend was used to assess whether there was an association between test-positivity and year. Results Of 52,789 patient testing events, 1467 (2.8%) were positive for gonorrhoea (81% male). Half (49.3%) of people (57.9% of males, 12.2% of females) with a gonorrhoea infection had an extragenital infection in the absence of a urogenital infection. The number of extragenital infections increased at a faster rate than urogenital among males. Test-positivity increased from 1.3% in 2012 to 5.8% in 2022 (P < 0.001). Antimicrobial resistance was identified in many isolates. Ciprofloxacin resistance was high, but there were no cases of ceftriaxone resistance. Conclusions This study highlights the importance of extragenital sampling and maintaining bacterial culture methods for accurate diagnosis and treatment. The observation that gonorrhoea positivity rate and antimicrobial resistance rates are rising in New Zealand calls for urgent action.Item A large chromosomal inversion affects antimicrobial sensitivity of Escherichia coli to sodium deoxycholate(Microbiology Society, 2022-08-12) Le VVH; León-Quezada RI; Biggs PJ; Rakonjac JResistance to antimicrobials is normally caused by mutations in the drug targets or genes involved in antimicrobial activation or expulsion. Here we show that an Escherichia coli strain, named DOC14, selected for increased resistance to the bile salt sodium deoxycholate, has no mutations in any ORF, but instead has a 2.1 Mb chromosomal inversion. The breakpoints of the inversion are two inverted copies of an IS5 element. Besides lowering deoxycholate susceptibility, the IS5-mediated chromosomal inversion in the DOC14 mutant was found to increase bacterial survival upon exposure to ampicillin and vancomycin, and sensitize the cell to ciprofloxacin and meropenem, but does not affect bacterial growth or cell morphology in a rich medium in the absence of antibacterial molecules. Overall, our findings support the notion that a large chromosomal inversion can benefit bacterial cells under certain conditions, contributing to genetic variability available for selection during evolution. The DOC14 mutant paired with its isogenic parental strain form a useful model as bacterial ancestors in evolution experiments to study how a large chromosomal inversion influences the evolutionary trajectory in response to various environmental stressors.Item Genomic Profiling of Mycobacterium tuberculosis Strains, Myanmar(Centers for Disease Control and Prevention, 2021-11) Aung HL; Nyunt WW; Fong Y; Biggs PJ; Winkworth RC; Lockhart PJ; Yeo TW; Hill PC; Cook GM; Aung STMultidrug resistance is a major threat to global elimination of tuberculosis (TB). We performed phenotypic drug-susceptibility testing and whole-genome sequencing for 309 isolates from 342 consecutive patients who were given a diagnosis of TB in Yangon, Myanmar, during July 2016‒June 2018. We identified isolates by using the GeneXpert platform to evaluate drug-resistance profiles. A total of 191 (62%) of 309 isolates had rifampin resistance; 168 (88%) of these rifampin-resistant isolates were not genomically related, indicating the repeated emergence of resistance in the population, rather than extensive local transmission. We did not detect resistance mutations to new oral drugs, including bedaquiline and pretomanid. The current GeneXpert MTB/RIF system needs to be modified by using the newly launched Xpert MTB/XDR cartridge or line-probe assay. Introducing new oral drugs to replace those currently used in treatment regimens for multidrug-resistant TB will also be useful for treating TB in Myanmar.