Jekyll and Hyde: The switch from environmental resident to antibiotic-resistant superbug in Pseudomonas aeruginosa

Pseudomonas aeruginosa strains embrace numerous strategies to enable their survival across a diverse range of environments. Historically, analysis of the core genome phylogeny has displayed five major clades one of which appeared distant from the other groups. This thesis presents detailed analysis of the divergent clade, characterised by the P. aeruginosa PA7 strain, to confirm the 16S rRNA sequence is identical to other P. aeruginosa strains and is unlike those belonging to other Pseudomonas spp. In contrast, methods utilising the whole genome reveals that this divergent group of PA7-like strains is distinctive enough to form its own separate species. Furthermore, detailed analysis of the P. aeruginosa core genome revealed groups of strains linked to either clinical or environmental origins. Niche associated core groups could be characterised by both gene presence and absence, as well as by single nucleotide polymorphisms. In terms of the clustering based on the P. aeruginosa accessory genome, few accessory clusters were spread across multiple core groups. This, coupled with a lack of gene flow between the core groups, suggests that the core genome provides a basis for niche adaption that is completed by the characteristics of the accessory genome. Additionally, this thesis sought to investigate how environmental P. aeruginosa isolates adapt to clinical niches by using the presence of chloramphenicol and ciprofloxacin antibiotics to simulate a clinical niche. This uncovered the trajectories taken by the organism to resist antibiotic pressure which involved “switching-on” intrinsically encoded efflux pumps. After the removal of antibiotic pressure, the efflux systems were “switched-off” by additional mutations. Whilst these mutations reduce antibiotic tolerance, they also alter fitness to varying degrees relative to the ancestral parent and mutant strains

Prevalence of new variants of Chlamydia trachomatis escaping detection by the Aptima Combo 2 assay, England, June to August 2019

At the end of April 2019, Public Health England (PHE) was alerted, via an international Epidemic Intelligence System-Sexually Transmitted Infections (EPIS-STI) post from Finland, of false-negative Chlamydia trachomatis (CT) test results using the Aptima Combo 2 (AC2) assay (Hologic Inc., San Diego, California, United States (US)), a nucleic acid amplification test (NAAT) for CT (target: 23S rRNA) and Neisseria gonorrhoeae (GC) (target: 16S rRNA). Discrepant results between the AC2 assay and the Aptima Chlamydia trachomatis assay (ACT) (target: 16S rRNA) were reported to have occurred primarily in specimens that had AC2 relative light units (RLU) from 20 to 84 [1]. These false-negative AC2 results [2,3] were attributed to a C1515T mutation in the CT 23S rRNA gene. In early June 2019, Hologic Inc. issued a Field Safety Notice (FSN) to AC2-using laboratories, recommending ACT reflex retesting of AC2 CT-negative with RLU ≥ 15, CT-equivocal, or GC-equivocal/-positive (if CT-negative/equivocal) specimens to ensure detection of the Finnish new variant CT strain (F-nvCT) [3]. A European Centre for Disease Prevention and Control (ECDC) rapid risk assessment recommended countries estimate the spread of F-nvCT to inform the need for patient recall and retesting [4]. Here we report results from an investigation coordinated by a multiagency incident management team (IMT) to ascertain the prevalence of new variants of Chlamydia trachomatis escaping detection by the Aptima Combo 2 assay in England

Increased exposure to extended-spectrum β-lactamase-producing multidrug-resistant Enterobacteriaceae through the consumption of chicken and sushi products

The aim of this study was to determine the occurrence and patterns of resistance of extended-spectrum β-lactamase (ESBL) producing Enterobacteriaceae in food products purchased in Navarra, northern Spain. A total of 174 samples of fish and chicken were analyzed from September 2015 to September 2016, including raw and ready-to-eat products: trout (n = 25), salmon (n = 28), panga (n = 13), chicken nuggets and chicken scalopes (n = 32), sushi (n = 31) and sliced cooked poultry (n = 45). Cefpodoxime-resistant strains were isolated on ChromID ESBL agar and further phenotypic (antimicrobial study on MicroScan© NM37 panel) and genotypic characterization (multiplex PCR, sequencing and multi-locus sequence typing, MLST) was performed to confirm and characterize ESBL producers. Raw chicken and sushi have been determined as the most risky products regarding transmission of ESBL-producing Enterobacteriaceae (occurrence 53.1% and 19.4%, respectively), while sliced cooked poultry products appear to be a safe product in this aspect. With regard to raw fish, prevalence in salmon was lower (3.6%) than in trout and panga (16.0%). Ninety-eight per cent of ESBL isolates (n = 50) show multidrug-resistant profiles, highlighting the high resistances against quinolones and tetracyclines observed in chicken isolates, as well as against ertapenem and chloramphenicol in sushi strains. Predominant β-lactamase type was SHV-12 (50.1%), followed by TEM-type (24.5%) and CTX-M (20.8%). In addition, CTX-M type was only detected in chicken products. The phylogenetic study showed the prevalence of groups A (35%), F (25%) and B1 (15%), usually related to nonvirulent strains. MLST E. coli isolates (n = 20) were grouped into 5 clonal complexes (CC) and 15 sequence types (ST), showing high clonal diversity. ST117 was the prevalent sequence type, while the human pathogen ST131 was not detected in this study. The high prevalence of ESBL-producing multidrug-resistant Enterobacteriaceae detected in products of widespread consumption such as chicken and sushi, increases the concern regarding human exposure to superbugs and encourages the need to improve surveillance of this public health issue