Outbreak of Pandoraea commovens Infections among Non-Cystic Fibrosis Intensive Care Patients, Germany, 2019-2021

Antibacterial Siderophores of Pandoraea Pathogens and Their Impact on the Diseased Lung Microbiota

Antibiotic-resistant bacteria of the genus Pandoraea, frequently acquired from the environment, are an emerging cause of opportunistic respiratory infections, especially in cystic fibrosis (CF) patients. However, their specialized metabolites, including niche and virulence factors, remained unknown. Through genome mining of environmental and clinical isolates of diverse Pandoraea species, we identified a highly conserved biosynthesis gene cluster (pan) that codes for a nonribosomal peptide synthetase (NRPS) assembling a new siderophore. Using bioinformatics-guided metabolic profiling of wild type and a targeted null mutant, we discovered the corresponding metabolites, pandorabactin A and B. Their structures and chelate (gallium) complexes were elucidated by a combination of chemical degradation, derivatization, NMR, and MS analysis. Metagenomics and bioinformatics of sputum samples of CF patients indicated that the presence of the pan gene locus correlates with the prevalence of specific bacteria in the lung microbiome. Bioassays and mass spectrometry imaging showed that pandorabactins have antibacterial activities against various lung pathogens (Pseudomonas, Mycobacterium, and Stenotrophomonas) through depleting iron in the competitors. Taken together, these findings offer first insight into niche factors of Pandoraea and indicate that pandorabactins shape the diseased lung microbiota through the competition for iron.

Pandoraea Infections in Humans-A Systematic Review

Background/Objectives:Pandoraea species are Gram-negative, aerobic, rod-shaped bacteria that belong to the Burkholderiaceae family and the Betaproteobacteria class. Despite their rare occurrence in the general population, they have been increasingly observed as the causes of infection in immunocompromised individuals or patients with severe comorbidities. The present review seeks to examine all documented cases of Pandoraea spp. infections in humans, focusing on data related to epidemiology, microbiology, antimicrobial susceptibility, treatment options, and mortality rates. Methods: A systematic review was conducted through a literature search of the PubMed/MedLine and Scopus databases. This review is subjected to certain limitations regarding the data accuracy or pathogen identification molecular techniques applied in the studies. Results: In total, 29 studies provided information on 43 patients with Pandoraea spp. infections. The mean age of the patients was 42 years, and 58% were male. Cystic fibrosis was these patients' most prevalent risk factor (39.5%). The most frequently reported types of infection were lower respiratory tract infections (74.41%) and bacteremia (30.23%), followed by infective endocarditis, pancreatitis, upper respiratory tract infection, and osteomyelitis (4.65%). P. apista was the most regularly isolated species (37.2%), while antimicrobial resistance was lower for carbapenems, especially for imipenem (17.14%). The most commonly administered antibiotics included carbapenems (82%), cephalosporins, and trimethoprim/sulfamethoxazole (35.89%). The infection outcome primarily depended on the type of infection; mortality rates were high (30.23%) and particularly elevated for bloodstream infections. The protocol for this review was registered in Prospero (ID: CRD42024579385). Conclusions: Due to Pandoraea's unique antimicrobial resistance pattern and capacity to induce severe infection, clinicians should include it when making a differential diagnosis, especially in patients with severe comorbidities and immunodeficiency.

Snakemake workflows for long-read bacterial genome assembly and evaluation

With the advancement of long-read sequencing technologies and their increasing use for bacterial genomics, several methods for generating genome assemblies from error-prone long reads have been developed. These are complemented by various tools for assembly polishing using either long reads, short reads, or reference genomes. End users are therefore left with a plethora of possible combinations of programs for obtaining a final trusted assembly. Hence, there is also a need to measure the completeness and accuracy of such assemblies, for which, again, several evaluation methods implemented in various programs are available. In order to automatically run multiple genome assembly and evaluation programs at once, I developed two workflows for the workflow management system Snakemake, which provide end users with an easy-to-run solution for testing various genome assemblies from their sequencing data. Both workflows use the conda packaging system, so there is no need for manual installation of each program.

Availability & Implementation

The workflows are available as open source software under the MIT license at github.com/pmenzel/ont-assembly-snake and github.com/pmenzel/score-assemblies.