1
|
Day J, Afshar B, Rowlands RS, Umer TS, Windsor H, Paukner S, Jensen JS, Spiller OB, Chalker VJ, Beeton ML. Phenotypic and genotypic antimicrobial susceptibility patterns of the emerging human respiratory pathogen Mycoplasma amphoriforme isolated from the UK and Denmark. J Antimicrob Chemother 2022; 77:3126-3129. [PMID: 36048620 PMCID: PMC9616542 DOI: 10.1093/jac/dkac293] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 08/04/2022] [Indexed: 11/14/2022] Open
Abstract
Objectives To determine the phenotypic and genotypic antibiotic susceptibility of Mycoplasma amphoriforme isolates recovered from patients in the UK and Denmark. Methods Seven isolates of M. amphoriforme were examined for antimicrobial susceptibility to seven antibiotics using the microbroth dilution assay in line with the CLSI guidelines for mycoplasmas. Each isolate was additionally subjected to WGS to identify resistance-associated mutations. Based on the consensus sequences from the genomic data, PCR primers were designed, and tested, for the amplification of the QRDR within the parC gene. Results Of the seven isolates investigated, four (57%) were resistant to moxifloxacin (0.5–1 mg/L) and levofloxacin (1–2 mg/L), compared with those that were susceptible (0.03–0.06 and 0.006 mg/L, respectively). Isolate H29 was resistant to five of the seven antibiotics tested: moxifloxacin, 0.5 mg/L; levofloxacin, 2 mg/L; azithromycin, 64 mg/L; erythromycin, 128 mg/L; and clindamycin, 64 mg/L. All isolates were susceptible to tetracycline (0.06 mg/L) and lefamulin (0.001–0.004 mg/L). Mutations from genomic data confirmed the presence of an S89F mutation within the ParC protein among all fluoroquinolone-resistant isolates and an A2059G mutation in the 23S rRNA gene in the macrolide- and lincosamide-resistant isolate H29. Conclusions To the best of our knowledge, this is the first time where phenotypic and genotypic resistance data have been paired for M. amphoriforme confirming a correlation between the two. These data suggest the need for focused testing and resistance determination of isolates from high-risk patients given the backdrop of a high prevalence of antimicrobial resistance.
Collapse
Affiliation(s)
- Jessica Day
- United Kingdom Health Security Agency, Colindale, London, UK
| | - Baharak Afshar
- United Kingdom Health Security Agency, Colindale, London, UK
| | - Richard S Rowlands
- Microbiology and Infection Research Group, Cardiff School of Sport and Health Sciences, Cardiff Metropolitan University, Cardiff, UK
| | - Taiba S Umer
- Microbiology and Infection Research Group, Cardiff School of Sport and Health Sciences, Cardiff Metropolitan University, Cardiff, UK
| | - Helena Windsor
- Mycoplasma Experience, Brewer Street Dairy Business Park, Bletchingley, Surrey, UK
| | | | - Jorgen S Jensen
- Research Unit for Reproductive Microbiology, Statens Serum Institut, Copenhagen, DK-2300, Denmark
| | - Owen B Spiller
- United Kingdom Health Security Agency, Colindale, London, UK.,Cardiff University, Division of Infection and Immunity, Department of Medical Microbiology, University Hospital of Wales, Cardiff, UK
| | | | - Michael L Beeton
- United Kingdom Health Security Agency, Colindale, London, UK.,Microbiology and Infection Research Group, Cardiff School of Sport and Health Sciences, Cardiff Metropolitan University, Cardiff, UK
| | | |
Collapse
|
2
|
Dennis TPW, Mable BK, Brunelle B, Devault A, Carter RW, Ling CL, Mmbaga BT, Halliday JEB, Oravcova K, Forde TL. Target-enrichment sequencing yields valuable genomic data for challenging-to-culture bacteria of public health importance. Microb Genom 2022; 8. [PMID: 35622897 PMCID: PMC9465068 DOI: 10.1099/mgen.0.000836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genomic data contribute invaluable information to the epidemiological investigation of pathogens of public health importance. However, whole-genome sequencing (WGS) of bacteria typically relies on culture, which represents a major hurdle for generating such data for a wide range of species for which culture is challenging. In this study, we assessed the use of culture-free target-enrichment sequencing as a method for generating genomic data for two bacterial species: (1) Bacillus anthracis, which causes anthrax in both people and animals and whose culture requires high-level containment facilities; and (2) Mycoplasma amphoriforme, a fastidious emerging human respiratory pathogen. We obtained high-quality genomic data for both species directly from clinical samples, with sufficient coverage (>15×) for confident variant calling over at least 80% of the baited genomes for over two thirds of the samples tested. Higher qPCR cycle threshold (Ct) values (indicative of lower pathogen concentrations in the samples), pooling libraries prior to capture, and lower captured library concentration were all statistically associated with lower capture efficiency. The Ct value had the highest predictive value, explaining 52 % of the variation in capture efficiency. Samples with Ct values ≤30 were over six times more likely to achieve the threshold coverage than those with a Ct > 30. We conclude that target-enrichment sequencing provides a valuable alternative to standard WGS following bacterial culture and creates opportunities for an improved understanding of the epidemiology and evolution of many clinically important pathogens for which culture is challenging.
Collapse
Affiliation(s)
- Tristan P. W. Dennis
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Barbara K. Mable
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | | | | | - Ryan W. Carter
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Clare L. Ling
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Blandina T. Mmbaga
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Jo E. B. Halliday
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Katarina Oravcova
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Taya L. Forde
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
- *Correspondence: Taya L. Forde,
| |
Collapse
|
3
|
Rehman SU, Day J, Afshar B, Rowlands RS, Billam H, Joseph A, Guiver M, Maddocks SE, Chalker VJ, Beeton ML. Molecular exploration for Mycoplasma amphoriforme, Mycoplasma fermentans and Ureaplasma spp. in patient samples previously investigated for Mycoplasma pneumoniae infection. Clin Microbiol Infect 2021; 27:1697.e1-1697.e5. [PMID: 34186210 DOI: 10.1016/j.cmi.2021.06.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 06/08/2021] [Accepted: 06/12/2021] [Indexed: 10/21/2022]
Abstract
OBJECTIVES To determine the presence and genotypic macrolide susceptibility of Mycoplasma amphoriforme, and the presence of Ureaplasma spp. and Mycoplasma fermentans among clinical samples from England previously investigated for Mycoplasma pneumoniae. METHODS Quantitative and conventional PCR methods were used to retrospectively screen a collection of 160 clinical samples previously submitted to Public Health England (PHE) for the detection of M. pneumoniae between October 2016 and December 2017. Samples which were positive for M. amphoriforme DNA were further investigated for mutations associated with genotypic macrolide resistance by sequencing domain V of the 23s rRNA. RESULTS M. amphoriforme was detected in 10/160 samples (6.3%), Ureaplasma parvum was detected in 4/160 samples (2.5%), and M. fermentans was not detected in any samples (0/160). Of the nine individuals (two samples were from the same patient) in which M. amphoriforme was detected, eight were male (age range 10-60 years) and one was female (age range 30-40 years). One individual with cystic fibrosis was positive for both M. amphoriforme and U. parvum. All M. amphoriforme DNA was genotypically susceptible to macrolides. CONCLUSIONS Mycoplasma amphoriforme was found in clinical samples, including lower respiratory tract samples of patients with pneumonia. In the absence of other respiratory pathogens, these data suggest a potential role for this organism in human disease, with no evidence of acquired macrolide resistance. Ureaplasma parvum was detected in cerebrospinal fluid and respiratory tract samples. These data suggest that there is a need to consider these atypical respiratory pathogens in future diagnostic investigations.
Collapse
Affiliation(s)
- Safi U Rehman
- Microbiology and Infection Research Group, Cardiff School of Sport and Health Sciences, Cardiff Metropolitan University, CF5 2YB, UK; Public Health England, UK
| | | | | | - Richard S Rowlands
- Microbiology and Infection Research Group, Cardiff School of Sport and Health Sciences, Cardiff Metropolitan University, CF5 2YB, UK
| | | | | | | | - Sarah E Maddocks
- Microbiology and Infection Research Group, Cardiff School of Sport and Health Sciences, Cardiff Metropolitan University, CF5 2YB, UK
| | | | - Michael L Beeton
- Microbiology and Infection Research Group, Cardiff School of Sport and Health Sciences, Cardiff Metropolitan University, CF5 2YB, UK; Public Health England, UK.
| |
Collapse
|
4
|
Gómez Rufo D, García Sánchez E, García Sánchez JE, García Moro M. [Clinical implications of the genus Mycoplasma]. REVISTA ESPANOLA DE QUIMIOTERAPIA 2021; 34:169-184. [PMID: 33735544 PMCID: PMC8179937 DOI: 10.37201/req/014.2021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Dentro del género Mycoplasma, las especies que tradicionalmente se han relacionado con cuadros infecciosos han sido principalmente M. pneumoniae, M. genitalium, M. hominis o U. urealyticum. Sin embargo, existen otras muchas que están implicadas y, que muchas veces, son desconocidas para los profesionales sanitarios. El objetivo de esta revisión es identificar todas las especies del género Mycoplasma que se han aislado en el hombre y determinar su participación en la patología infecciosa humana.
Collapse
Affiliation(s)
| | - E García Sánchez
- Enrique García Sánchez, Departamento de Ciencias Biomédicas. Facultad de Medicina. Universidad de Salamanca. Spain.
| | | | | |
Collapse
|