High incidence of carbapenemase-producing Pseudomonas aeruginosa clinical isolates from Lagos, Nigeria.

Background: Carbapenem-resistant Pseudomonas aeruginosa strains are on the rise worldwide. This study characterized clinical isolates of P. aeruginosa from three Nigerian hospitals for carbapenem resistance. Methods: Strains isolated from wounds (n = 88), urine/catheter tips (n = 25), sputum/tracheotomy aspirates (n = 5), ear swabs (n = 4) and vaginal swabs (n = 1) were identified by MALDI-TOF and antibiotic susceptibility testing was performed using the VITEK 2 system. The genomic DNA of each isolate was subject to sequencing using Illumina and Oxford nanopore technology. Bioinformatics analyses were performed to detect antimicrobial resistance genes, clonal affiliations and phylogenetic relations of 123 non-duplicate P. aeruginosa isolates, whereas assembly of the nanopore reads using the plasmIDent pipeline enabled the identification of plasmids. Results: Forty-three percent of the isolates were resistant to all antibiotic categories tested. More than 40% of the isolates were resistant to the carbapenems imipenem and/or meropenem (39% and 44%, respectively). Among the meropenem-resistant isolates, 48 (89%) carried at least one carbapenemase gene. The predominant one was bla NDM-1 (n = 34), which conferred resistance to all five antibiotic categories and highly increased the MICs of both meropenem and imipenem. The other recurrent carbapenemase genes were bla VIM-2 (n = 4), and bla VIM-5-like (n = 11), which co-existed with bla NDM-1 in two isolates. Conclusions: The study revealed a high rate of carbapenem resistance and conjugative, broad host range plasmids carrying carbapenemase-encoding genes, especially the NDM-1 type, among isolates of P. aeruginosa. This may forebode the emergency of ubiquitous carbapenem resistance urging the implementation of infection control and antimicrobial stewardship strategies in Nigerian hospitals.

High prevalence of Pseudomonas aeruginosa carriage in residents of French and German long-term care facilities.

OBJECTIVES: To determine prevalence, incidence, and factors associated with Pseudomonas aeruginosa (PA) intestinal carriage in residents of long-term care facilities (LTCFs) and to understand the population structure of this pathogen in LTCFs from two European countries. METHODS: We assessed the prevalence of PA intestinal carriage and the incidence of acquisition by collecting fecal samples from 403 residents of 20 LTCFs. We collected 289 environmental samples from sinks and drinking water. Factors associated with carriage and acquisition of intestinal PA were identified. All PA isolates had their antibiotic phenotypic resistance profile determined and their genome sequenced, from which we assessed the population structure of the collection and identified resistance determinants. RESULTS: We found a high proportion of residents with PA intestinal carriage (51.6%) over the entire study period. Over the follow-up period, 28.6% of the residents acquired intestinal PA. Older age (OR, 1.29; 95% CI, 1.09-1.52; p = 0.002), urinary incontinence (OR, 2.56; 95% CI, 1.37-4.88; p = 0.003), and male sex (OR, 2.55; 95% CI, 1.05-6.18; p = 0.039) were associated with higher probability of carriage. Wheelchair usage (OR, 4.56; 95% CI, 1.38-15.05; p = 0.013) and a body mass index >25 (OR, 3.71; 95% CI, 1.17-11.82; p = 0.026) were associated with higher risk of PA acquisition. Population structure of our isolates was mainly non-clonal with 112 different STs among the 241 isolates. Most represented STs were high risk clones ST253 (n = 26), ST17 (n = 11), ST244 (n = 11), ST309 (n = 10), and ST395 (n = 10). Most PA isolates (86.3%) were susceptible to antibiotics, with no acquired genes conferring resistance to antipseudomonal agents. DISCUSSION: We found an unexpected high prevalence of PA intestinal carriage in LTCF residents mainly associated with individual-level factors. Our study revealed a polyclonal PA population structure suggesting that individual acquisition is more frequent than resident-to-resident transmission.

Populations of extended-spectrum ß-lactamase-producing Escherichia coli and Klebsiella pneumoniae are different in human-polluted environment and food items: a multicentre European study.

OBJECTIVES: To assess the extent to which food items are a source of extended-spectrum ß-lactamase (ESBL) -producing Escherichia coli (ESBL-Ec) and ESBL-producing Klebsiella pneumoniae (ESBL-Kp) for humans in five European cities. METHODS: We sampled 122 human polluted (hp)-environments (sewers and polluted rivers, as a proxy of human contamination) and 714 food items in Besançon (France), Geneva (Switzerland), Sevilla (Spain), Tübingen (Germany) and Utrecht (The Netherlands). A total of 254 ESBL-Ec and 39 ESBL-Kp isolates were cultured. All genomes were fully sequenced to compare their sequence types (ST) and core genomes, along with the distribution of blaESBL genes and their genetic supports (i.e. chromosome or plasmid). RESULTS: Sequence data revealed that ESBL-Ec and ESBL-Kp isolates from hp-environments were genetically different from those contaminating food items. ESBL-Ec ST131 was widespread in the hp-environment (21.5% of the isolates) but absent from the food items tested. ESBL-Ec ST10 was in similar proportions in hp-environments and food items (15 and 10 isolates, respectively) but mostly carried reservoir-specific blaESBL. blaCTX-M-1 and blaSHV-12 predominated in food-related E. coli isolates (32% and 34% of the isolates, respectively), whereas blaCTX-M-15 and blaCTX-M-27 predominated in isolates from hp-environments (52% and 15% of the isolates, respectively). CONCLUSIONS: We found a very limited connection between ESBL-Ec and ESBL-Kp populations retrieved in food items and from hp-environments and blaESBL. This suggests that human-to-human contamination, rather than the food chain, is possibly the most frequent route of ESBL-Ec and ESBL-Kp transmission in high-income countries.

Household acquisition and transmission of extended-spectrum ß-lactamase (ESBL) -producing Enterobacteriaceae after hospital discharge of ESBL-positive index patients.

OBJECTIVES: This study aimed to determine rates and risk factors of extended-spectrum ß-lactamase-producing Enterobacteriaceae (ESBL-PE) acquisition and transmission within households after hospital discharge of an ESBL-PE-positive index patient. METHODS: Two-year prospective cohort study in five European cities. Patients colonized with ESBL-producing Escherichia coli (ESBL-Ec) or Klebsiella pneumoniae (ESBL-Kp), and their household contacts were followed up for 4 months after hospital discharge of the index case. At each follow up, participants provided a faecal sample and personal information. ESBL-PE whole-genome sequences were compared using pairwise single nucleotide polymorphism-based analysis. RESULTS: We enrolled 71 index patients carrying ESBL-Ec (n = 45), ESBL-Kp (n = 20) or both (n = 6), and 102 household contacts. The incidence of any ESBL-PE acquisition among household members initially free of ESBL-PE was 1.9/100 participant-weeks at risk. Nineteen clonally related household transmissions occurred (case to contact: 13; contact to case: 6), with an overall rate of 1.18 transmissions/100 participant-weeks at risk. Most of the acquisition and transmission events occurred within the first 2 months after discharge. The rate of ESBL-Kp household transmission (1.16/100 participant-weeks) was higher than of ESBL-Ec (0.93/100 participant-weeks), whereas more acquisitions were noted for ESBL-Ec (1.06/100 participant-weeks) compared with ESBL-Kp (0.65/100 participant-weeks). Providing assistance for urinary and faecal excretion to the index case by household members increased the risk of ESBL-PE transmission (adjusted prevalence ratio 4.3; 95% CI 1.3-14.1). CONCLUSIONS: ESBL-PE cases discharged from the hospital are an important source of ESBL-PE transmission within households. Most acquisition and transmission events occurred during the first 2 months after hospital discharge and were causally related to care activities at home, highlighting the importance of hygiene measures in community settings. CLINICAL STUDY REGISTRATION: German Clinical Trials Register, DRKS-ID: DRKS00013250.

Evaluation of three fully-automated SARS-CoV-2 antibody assays.

Objectives Serological assays for detection of SARS-CoV-2 antibodies are increasingly used during the COVID-19 pandemic caused by the SARS-Coronavirus-2. Here we evaluated the analytical and clinical performance of three commercially available SARS-CoV-2 antibody assays. Methods A total of 186 samples from 58 patients with PCR-confirmed COVID-19 infection were measured using SARS-CoV-2 antibody assays by Siemens Healthineers, Roche Diagnostics and Euroimmun. Additionally, 123 control samples, including samples collected before December 2019 and samples with potential cross-reactive antibodies were analyzed. Diagnostic specificity, sensitivity, agreement between assays and ROC curve-derived optimized thresholds were determined. Furthermore, intra- and inter-assay precision and the potential impact of interfering substances were investigated. Results SARS-CoV-2 antibody assays by Siemens and Roche showed 100% specificity. The Euroimmun assay had 98 and 100% specificity, when borderline results are considered as positive or negative, respectively. Diagnostic sensitivity for samples collected ≥14 days after PCR-positivity was 97.0, 89.4 and 95.5% using the Siemens, Roche and Euroimmun assay, respectively. Sensitivity of the Roche assay can be increased using an optimized cut-off index (0.095). However, a simultaneous decrease in specificity (98.4%) was observed. Siemens showed 95.8 and 95.5% overall agreement with results of Euroimmun and Roche assay, respectively. Euroimmun and Roche assay exhibited 92.6% overall agreement. Discordant results were observed in three COVID-19 patients and in one COVID-19 patient none of the investigated assays detected antibodies. Conclusions The investigated assays were highly specific and sensitive in detecting SARS-CoV-2 antibodies in samples obtained ≥14 days after PCR-confirmed infection. Discordant results need to be investigated in further studies.