Investigating Pseudomonas aeruginosa population structure and frequency of cross-infection in UK cystic fibrosis clinics - a reference laboratory perspective.

BACKGROUND: We aimed to describe the UK Pseudomonas aeruginosa population structure amongst people with cystic fibrosis (PWCF), and to examine evidence for cross-infection. METHODS: Variable Number Tandem Repeat (VNTR) typing was performed on 4640 isolates from 2619 PWCF received from 55 hospital laboratories between 2017 and 2019. A combination of whole genome sequence (WGS)-based analysis of four clusters from one hospital, and epidemiological analysis of shared strains in twelve hospitals evaluated cross-infection. RESULTS: Of 2619 PWCF, 1324 (51%) harboured common clusters or known transmissible strains, while 1295 carried unique strains/those shared among small numbers of patients. Of the former, 9.5% (250 patients) harboured the Liverpool epidemic strain (LES), followed in prevalence by clone C (7.8%; 205 patients), cluster A (5%;130 patients), and cluster D (3.6%; 94 patients). WGS analysis of 10 LES isolates, 9 of cluster D and 6 isolates each of cluster A and clone C from one hospital revealed LES formed the tightest cluster (between 7 and 205 SNPs), and cluster D the loosest (between 53 and 1531 SNPs). Hospital-specific shared strains were found in some centres, although cross-infection was largely historical, with few new acquisitions. Fifty-nine PWCF (2.3%) harboured "high-risk" clones; one ST235 isolate carried a blaIMP-1 allele. CONCLUSION: Of 2619 PWCF who had P. aeruginosa isolates submitted for VNTR, 51% harboured either common clusters or known transmissible strains, of which LES was the most common. Limited evidence of recent patient-to-patient strain transmission was found, suggesting cross-infection prevention measures and surveillance effectively reduce transmission.

Hybrid Resistance and Virulence Plasmids in "High-Risk" Clones of Klebsiella pneumoniae, Including Those Carrying blaNDM-5.

Virulence plasmids are associated with hypervirulent types of Klebsiella pneumoniae, which generally do not carry antibiotic resistance genes. In contrast, nosocomial isolates are often associated with resistance, but rarely with virulence plasmids. Here, we describe virulence plasmids in nosocomial isolates of "high-risk" clones of sequence types (STs) 15, 48, 101, 147 and 383 carrying carbapenemase genes. The whole genome sequences were determined by long-read nanopore sequencing. The 12 isolates all contained hybrid plasmids containing both resistance and virulence genes. All carried rmpA/rmpA2 and the aerobactin cluster, with the virulence plasmids of two of three representatives of ST383 carrying blaNDM-5 and seventeen other resistance genes. Representatives of ST48 and ST15 had virulence plasmid-associated genes distributed between two plasmids, both containing antibiotic resistance genes. Representatives of ST101 were remarkable in all sharing virulence plasmids in which iucC and terAWXYZ were missing and iucB and iucD truncated. The combination of resistance and virulence in plasmids of high-risk clones is extremely worrying. Virulence plasmids were often notably consistent within a lineage, even in the absence of epidemiological links, suggesting they are not moving between types. However, there was a common segment containing multiple resistance genes in virulence plasmids of representatives of both STs 48 and 383.

Virulence genes in isolates of Klebsiella pneumoniae from the UK during 2016, including among carbapenemase gene-positive hypervirulent K1-ST23 and 'non-hypervirulent' types ST147, ST15 and ST383.

PURPOSE: Klebsiella pneumoniae is a concern because of its multidrug resistance and the ability of hypervirulent types, especially capsular type K1-clonal complex 23 (K1-CC23), to cause community-acquired, life-threatening infections. Hypervirulent types carry an array of virulence genes including rmpA/rmpA2, coding for capsule up-regulation. We sought to identify isolates carrying these elements among submissions to the UK national reference laboratory during 2016. METHODOLOGY: Virulence elements and carbapenemase genes were sought by PCR or from whole genome sequences. Isolates were typed by variable number tandem repeat analysis or by multi locus sequence typing from whole genome sequences. Long read nanopore sequencing was carried out on two isolates.Results/Key findings. Twelve of 1090 isolates (1.1 %) belonged to hypervirulent K1-CC23, with one carrying blaOXA-48 (KpvST23L_OXA-48). A further 24 rmpA/rmpA2-positive isolates were detected: eight belonged to hypervirulent types of capsular types K2 and K54; and 14 belonged to 'non-hypervirulent' ST147, ST15 and ST383 and also carried carbapenemase gene(s). Virulence, heavy metal and antibiotic resistance gene contents were compared from whole genome sequences of KpvST23L_OXA-48 and one of the ST147 isolates carrying blaNDM-1. They carried 94/96 and 26/96 of the virulence genes sought, and 23/23 and 9/23 of the heavy metal resistance genes, respectively. In the ST147 isolate, rmpA/rmpA2 and the aerobactin siderophore cluster were on a large virulence plasmid together with resistance genes. The yersiniabactin cluster was widely present among carbapenemase gene-positive isolates, including among those that were rmpA/rmpA2-negative. CONCLUSION: Our results highlight a combination of virulence and resistance genes, which could lead to untreatable invasive infections.