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While most influenza patients have a self-limited respiratory illness, 5–10% of hospitalized patients develop severe disease requiring ICU admission. The aim of this study was to identify influenza-specific factors associated with ICU admission and mortality. Furthermore, influenza-specific pulmonary bacterial, fungal and viral co-infections were investigated. 199 influenza patients, admitted to two academic hospitals in the Netherlands between 01-10-2015 and 01-04-2016 were investigated of which 45/199 were admitted to the ICU. A history of Obstructive/Central Sleep Apnea Syndrome, myocardial infarction, dyspnea, influenza type A, BMI > 30, the development of renal failure and bacterial and fungal co-infections, were observed more frequently in patients who were admitted to the ICU, compared with patients at the normal ward. Co-infections were evident in 55.6% of ICU-admitted patients, compared with 20.1% of patients at the normal ward, mainly caused by Staphylococcus aureus, Streptococcus pneumoniae, and Aspergillus fumigatus. Non-survivors suffered from diabetes mellitus and (pre-existent) renal failure more often. The current study indicates that a history of OSAS/CSAS, myocardial infarction and BMI > 30 might be related to ICU admission in influenza patients. Second, ICU patients develop more pulmonary co-infections. Last, (pre-existent) renal failure and diabetes mellitus are more often observed in non-survivors. •A history of OSAS/CSAS, myocardial infarction and BMI > 30 are risk factors for ICU admission.•Non-survivors suffer more often from diabetes mellitus and (pre-existent) renal failure.•ICU patients develop renal failure and bacterial/fungal co-infections more often.

Background Post-operative infections are frequent after radical cystectomy with urinary diversion surgery (UDS). Reduction of post-operative infections necessitates appropriate peri-operative antimicrobial prophylaxis targeting causative bacteria. We assessed the incidence and microbiology of infections in the 30-day post-operative period after UDS and investigated effectiveness of the currently used peri-operative antibacterial prophylaxis. Methods Retrospective cohort study of all patients undergoing UDS in a tertiary university medical center from January 2014 until September 2016. Antibiotic prophylaxis consisted of cefazolin plus metronidazol according to the Dutch national guideline. Primary outcome was the incidence of post-operative infections within 30 days. Risk factors for post-operative infections and antimicrobial susceptibility profiles of cultured bacteria were also assessed. Results 147 patients were included. 69 patients (46.9%) had 82 post-operative infections, 27 of which were patients with bacteremia (18.4%). Highest incidence of infections was on day 4–5 and on day 8–10 postoperatively. The second peak was associated with ureteral stent removal. 4.8% of 147 study patients developed bacteremia 24 h after stent removal, which counted for 25.9% of all bacteremia episodes found in this study. Enterobacteriaceae were cultured in 67.9% of blood cultures and were only highly susceptible to ciprofloxacine, piperacillin-tazobactam (90%), meropenem and gentamicin (100%). Multivariate logistic regression analysis showed orthotopic Hautmann neobladder to be associated with increased infections complications: odds ratio 4.1 (95% confidence interval 1.6–10.5), p  = 0.03. Conclusions The incidence of infections after radical cystectomy is high and particularly ureteral stent removal was associated with both bacteremia and complicated urinary tract infections. Based on the results of this study, antibiotic prophylaxis might need to be broadened for patients undergoing radical cystectomy. Further research is required to investigate whether current guidelines need to be altered concerning administration of antibiotic prophylaxis just before stent removal.

Background Multidrug-resistant organisms (MDRO) pose a significant threat to public health worldwide. The ability to identify antimicrobial resistance determinants, to assess changes in molecular types, and to detect transmission are essential for surveillance and infection prevention of MDRO. Molecular characterization based on long-read sequencing has emerged as a promising alternative to short-read sequencing. The aim of this study was to characterize MDRO for surveillance and transmission studies based on long-read sequencing only. Methods Genomic DNA of 356 MDRO was automatically extracted using the Maxwell-RSC48. The MDRO included 106 Klebsiella pneumoniae isolates, 85 Escherichia coli , 15 Enterobacter cloacae complex, 10 Citrobacter freundii , 34 Pseudomonas aeruginosa , 16 Acinetobacter baumannii , and 69 methicillin-resistant Staphylococcus aureus (MRSA), of which 24 were from an outbreak. MDRO were sequenced using both short-read (Illumina NextSeq 550) and long-read (Nanopore Rapid Barcoding Kit-24-V14, R10.4.1) whole-genome sequencing (WGS). Basecalling was performed for two distinct models using Dorado-0.3.2 duplex mode. Long-read data was assembled using Flye, Canu, Miniasm, Unicycler, Necat, Raven, and Redbean assemblers. Long-read WGS data with > 40 × coverage was used for multi-locus sequence typing (MLST), whole-genome MLST (wgMLST), whole-genome single-nucleotide polymorphisms (wgSNP), in silico multiple locus variable-number of tandem repeat analysis (iMLVA) for MRSA, and identification of resistance genes (ABRicate). Results Comparison of wgMLST profiles based on long-read and short-read WGS data revealed > 95% of wgMLST profiles within the species-specific cluster cut-off, except for P. aeruginosa . The wgMLST profiles obtained by long-read and short-read WGS differed only one to nine wgMLST alleles or SNPs for K. pneumoniae , E. coli , E. cloacae complex, C. freundii , A. baumannii complex, and MRSA. For P. aeruginosa , differences were up to 27 wgMLST alleles between long-read and short-read wgMLST and 0–10 SNPs. MLST sequence types and iMLVA types were concordant between long-read and short-read WGS data and conventional MLVA typing. Antimicrobial resistance genes were detected in long-read sequencing data with high sensitivity/specificity (92–100%/99–100%). Long-read sequencing enabled analysis of an MRSA outbreak. Conclusions We demonstrate that molecular characterization of automatically extracted DNA followed by long-read sequencing is as accurate compared to short-read sequencing and suitable for typing and outbreak analysis as part of genomic surveillance of MDRO. However, the analysis of P. aeruginosa requires further improvement which may be obtained by other basecalling algorithms. The low implementation costs and rapid library preparation for long-read sequencing of MDRO extends its applicability to resource-constrained settings and low-income countries worldwide.

We investigated the genomic epidemiology of Ambler class C (AmpC-type) β-lactamases in Enterobacter cloacae complex and Klebsiella aerogenes in the national carbapenemase-producing Enterobacterales (CPE) surveillance of the Netherlands between 2012 and 2023. A total of 399 E. cloacae complex and K. aerogenes isolates from 399 patients were analyzed using whole-genome sequencing to assess genetic relatedness, resistance genes, porin, and AmpC-regulatory gene profiles, plasmid replicons, and the genomic location of AmpC-genes, respectively. Of the 399 patients, 217 were male (54%), and the median age was 67 years. Carbapenemase production was assessed using the carbapenem inactivation method (CIM) and CarbaNP-test. A considerable proportion of E. cloacae complex (32%) and K. aerogenes (52%) isolates were CIM-positive in the absence of detectable carbapenemase genes (IMP, KPC, NDM, OXA-48-like, VIM) by the CarbaPCR, a phenotype termed CIM + Carba-. These isolates were mostly (81.9%) susceptible (EUCAST ≤ 2mg/L) to meropenem. The majority of CIM + Carba + isolates with major carbapenemase genes were gained from pre-emptive screening, while CIM + Carba- isolates were mainly taken for diagnostic purposes. Genomic analysis identified 18 genogroups, with E. kobei , E. roggenkampii , E. ludwigii, and K. aerogenes showing the CIM + Carba- phenotype, were mostly lacking porins and AmpC regulators, and correlated with chromosome-encoded AmpC-type β-lactamases like bla ACT-28 , bla ACT-52, bla MIR-3 , bla MIR-11 or ampC of which the majority (63%) yielded a positive CarbaNP-test. These CIM + Carba- isolates carried only few plasmids, and there was limited evidence of nosocomial spread. CIM + Carba- E. kobei carrying bla ACT-28 overproduced ACT-28 protein in the CIM. Overall, the Enterobacter and K. aerogenes population in the Netherlands is genetically diverse, with most isolates carrying species-specific AmpC-type β-lactamases. Isolates with low MIC for meropenem that lack porins and major carbapenemases represent a low-risk for public health.

Background Although the Netherlands is a country with a low endemic level of methicillin-resistant Staphylococcus aureus (MRSA), a national MRSA surveillance has been in place since 1989. In 2003 livestock emerged as a major reservoir of MRSA and currently livestock-associated MRSA (clonal complex CC398) make up 25% of all surveillance isolates. To assess possible transfer of resistant strains or resistance genes, MRSA obtained from humans and animals were characterized in detail. Methods The sequenced genomes of 6327 MRSA surveillance isolates from humans and from 332 CC398 isolates from livestock-related samples were analyzed and resistance genes were identified. Several isolates were subjected to long-read sequencing to reconstruct chromosomes and plasmids. Results Here we show the presence of the multi-resistance gene cfr in seven CC398 isolates obtained from humans and in one CC398 isolate from a pig-farm dust sample. Cfr induces resistance against five antibiotic classes, which is true for all but two isolates. The isolates are genetically unrelated, and in seven of the isolates cfr are located on distinct plasmids. The fexA gene is found in 3.9% surveillance isolates and in 7.5% of the samples from livestock. There is considerable sequence variation of fexA and geographic origin of the fexA alleles. Conclusions The rare cfr and fexA resistance genes are found in MRSA from humans and animals in the Netherlands, but there is no evidence for spread of resistant strains or resistance plasmids. The proportion of cfr -positive MRSA is low, but its presence is worrying and should be closely monitored. Plain language summary A group of bacteria that cause difficult-to-treat infections in humans is methicillin-resistant Staphylococcus aureus (MRSA). Monitoring the spread of MRSA strains and genes that cause antibiotic resistance is important for appropriate intervention. In the Netherlands, 25% of MRSA isolates from patients are MRSA types often found in livestock (LA-MRSA). In this study we have identified the cfr gene in a small number of LA-MRSA obtained from humans and animals. The cfr gene causes resistance to five antibiotic classes, including the last resort antibiotic linezolid. We also found that MRSA from humans and animals carried the antibiotic resistance gene fexA and these were often also LA-MRSA. The results suggest that these resistance genes originate from livestock and were transferred to humans. Large scale antibiotic treatment of livestock may lead to increased antibiotic resistance in MRSA found in humans. Schouls et al. characterize antimicrobial resistance genes in MRSA isolates from humans and livestock in the Netherlands. The multidrug resistance gene cfr and the phenicol resistance gene fexA are identified in both types of samples, including in samples taken from persons having professional contact with livestock.

We studied nosocomial transmission of multidrug-resistant bla NDM-1 -containing Klebsiella pneumoniae ST147 in a Dutch pediatric oncology center. Whole-genome multilocus sequence typing revealed two genetic clusters consisting of 2 and 5 K. pneumoniae isolates, both from Ukrainian medical evacuees and Dutch patients. Ukrainian patients were colonized at admission, and two Dutch patients developed bacteremia. Temporal and spatial transmission links were assessed and sampling of sinks revealed environmental contamination of bla NDM-1 -containing K. pneumoniae with genetic relatedness to cluster isolates. Phylogenetic analysis of 163 K. pneumoniae ST147 isolates from the Dutch national surveillance revealed that transmission-related isolates formed a unique phylogenetic branch. In conclusion, we demonstrate nosocomial transmission of unique bla NDM-1 -containing K. pneumoniae ST147 strains introduced by Ukrainian patients. Sink drains colonized by genetically similar bla NDM-1 -containing strains in rooms designated as spatial links within the cluster were considered the potential source of transmission. Healthcare professionals should be aware of these risks, particularly in settings with susceptible patients exposed to antibiotic pressure.

We observed an increase in methicillin-susceptible Staphylococcus aureus (MSSA) infections at a Dutch neonatal intensive care unit. Weekly neonatal MSSA carriage surveillance and cross-sectional screenings of health care workers (HCWs) were available for outbreak tracing. Traditional clustering of MSSA isolates by spa typing and Multiple-Locus Variable number tandem repeat Analysis (MLVA) suggested that nosocomial transmission had contributed to the infections. We investigated whether whole-genome sequencing (WGS) of MSSA surveillance would provide additional evidence for transmission. MSSA isolates from neonatal infections, carriage surveillance, and HCWs were subjected to WGS and bioinformatic analysis for identification and localization of high-quality single nucleotide polymorphisms, and in-depth analysis of subsets of isolates. By measuring the genetic diversity in background surveillance, we defined transmission-level relatedness and identified isolates that had been unjustly assigned to clusters based on MLVA, while spa typing was concordant but of insufficient resolution. Detailing particular subsets of isolates provided evidence that HCWs were involved in multiple outbreaks, yet it alleviated concerns about one particular HCW. The improved resolution and accuracy of genomic outbreak analyses substantially altered the view on outbreaks, along with apposite measures. Therefore, inclusion of the circulating background population has the potential to overcome current issues in genomic outbreak inference.

Abstract Background Little is known about the presence of resistant micro-organisms in people with intellectual disabilities (ID) residing in long-term care facilities (LTCFs). We explored the resistant percentages of six highly resistant micro-organisms (HRMOs) among people with ID in ID-LTCFs: ESBL-producing Enterobacterales (ESBL-E), carbapenemase-producing Enterobacterales (CPE), Acinetobacter spp. (CPA) and Pseudomonas aeruginosa (CPPA), MRSA and VRE. Methods We included data on the first isolate per species, per patient, per year ordered by ID physicians, as delivered by 11 clinical microbiology laboratories, participating in the Dutch National Infectious Diseases Surveillance Information System-Antimicrobial Resistance (ISIS-AR) between 2018 and 2023. Resistance was classified based on phenotypic and genotypic test results. The resistance percentage for each HRMO was calculated as the percentage of resistant isolates among the total number of isolates for each corresponding species. Results The percentage of resistant ESBL-E isolates among Enterobacterales isolates was 3.2% (95% CI: 2.5%–4.0%), CPPA among P. aeruginosa isolates was 1.3% (0.4%–3.8%) and MRSA among Staphylococcus aureus isolates 0.4% (0.01%–2.35%). No CPE (ntested = 2242), CPA (ntested = 25) and VRE (ntested = 6) were found. Conclusions The resistance percentages for six HRMOs among positive diagnostic isolates ordered by ID physicians for people with ID in the Netherlands are low. The majority of HRMOs detected were isolated from older adults with ID. To estimate the burden of AMR and associated risk factors in the whole ID population, more extensive studies, including data from other medical specialties serving people with ID, such as general practitioners, are needed.

Background. Although the Netherlands is a country with a low endemic level, methicillin-resistant Staphylococcus aureus (MRSA) poses a significant health care problem. Therefore, high coverage national MRSA surveillance has been in place since 1989. To monitor possible changes in the type-distribution and emergence of resistance and virulence, MRSA isolates are molecularly characterized. Methods. All 43,321 isolates from 36,520 persons, collected 2008–2019, were typed by multiple-locus variable number tandem repeats analysis (MLVA) with simultaneous PCR detection of the mecA , mecC and lukF-PV genes, indicative for PVL. Next-generation sequencing data of 4991 isolates from 4798 persons were used for whole genome multi-locus sequence typing (wgMLST) and identification of resistance and virulence genes. Results. We show temporal change in the molecular characteristics of the MRSA population with the proportion of PVL-positive isolates increasing from 15% in 2008–2010 to 25% in 2017–2019. In livestock-associated MRSA obtained from humans, PVL-positivity increases to 6% in 2017–2019 with isolates predominantly from regions with few pig farms. wgMLST reveals the presence of 35 genogroups with distinct resistance, virulence gene profiles and specimen origin. Typing shows prolonged persistent MRSA carriage with a mean carriage period of 407 days. There is a clear spatial and a weak temporal relationship between isolates that clustered in wgMLST, indicative for regional spread of MRSA strains. Conclusions. Using molecular characterization, this exceptionally large study shows genomic changes in the MRSA population at the national level. It reveals waxing and waning of types and genogroups and an increasing proportion of PVL-positive MRSA. Plain language summary A group of bacteria that cause difficult-to-treat infections in humans is methicillin-resistant Staphylococcus aureus (MRSA). The aim of this study was to monitor changes in the spread of MRSA, their disease causing potential and resistance to antibiotics used to treat MRSA infections. MRSA from patients and their contacts in the Netherlands were collected over a period of 12 years and characterized. This revealed new types of MRSA emerged and others disappeared. An increasing number of MRSA produces a protein called PVL toxin, enabling MRSA to cause more severe infections. Also, some people appear to carry MRSA without any disease for more than a year. These findings suggest an increasing disease potential of MRSA and possible unnoticed sources of infection. Consequently, it is important to maintain monitoring of these infections to minimize MRSA spread. Schouls et al. characterize 43,321 methicillin-resistant Staphylococcus aureus (MRSA) isolates obtained between 2008 and 2019 in the Netherlands. Genomic changes occur in the MRSA population, with increases in the proportion of PVL-positive MRSA.

Background The Netherlands is currently considered a low endemic country for carbapenem-resistant Enterobacterales (CRE) and carbapenemase-producing Enterobacterales (CPE), experiencing only sporadic hospital outbreaks. This study aims to describe susceptibility to carbapenems and the epidemiology of carbapenemase production in Enterobacterales in the Netherlands in 2017–2019. Methods Three complementary nationwide surveillance systems are in place to monitor carbapenem susceptibility in the Netherlands. Routine antimicrobial susceptibility test results from medical microbiology laboratories were used to study phenotypic susceptibility of Escherichia coli and Klebsiella pneumoniae . Pathogen surveillance (of all Enterobacterales species) and mandatory notifications were used to describe the characteristics of CPE positive isolates and affected persons. Results The prevalence of isolates with gradient strip test-confirmed elevated meropenem (> 0.25 mg/L) or imipenem (> 1 mg/L) minimum inhibitory concentration (MIC) in the Netherlands was very low in 2017–2019, with percentages of 0.06% in E. coli and 0.49% in K. pneumoniae , and carbapenem resistances of 0.02% and 0.18%, respectively. A total of 895 unique species/carbapenemase-encoding allele combinations of CPE from 764 persons were submitted between 2017 and 2019, with the annual number of submissions increasing slightly each year. Epidemiological data was available for 660 persons. Screening because of presumed colonisation risk was the reason for sampling in 70.0% (462/660) of persons. Hospitalization abroad was the most common risk factor, being identified in 45.9% of persons. Conclusions Carbapenem resistance of E. coli and K. pneumoniae remains low in the Netherlands. The annual number of CPE isolates slightly increased during the period 2017–2019. Recent hospitalization abroad is the main risk factor for acquisition of CPE.