Genotypic resistance determined by whole genome sequencing versus phenotypic resistance in 234 Escherichia coli isolates.

Whole genome sequencing (WGS) enables detailed characterization of bacteria at single nucleotide resolution. It provides data about acquired resistance genes and mutations leading to resistance. Although WGS is becoming an essential tool to predict resistance patterns accurately, comparing genotype to phenotype with WGS is still in its infancy. Additional data and validation are needed. In this retrospective study, we analysed 234 E. coli isolates from positive blood cultures using WGS as well as microdilution for 11 clinically relevant antibiotics, to compare the two techniques. We performed whole genome sequencing analyses on 234 blood culture isolates (genotype) to detect acquired antibiotic resistance. Minimal inhibitory concentrations (MIC) for E. coli were performed for amoxicillin, cefepime, cefotaxime, ceftazidime, meropenem, amoxicillin/clavulanic acid, piperacillin/tazobactam, amikacin, gentamicin, tobramycin, and ciprofloxacin, using the ISO 20776-1 standard broth microdilution method as recommended by EUCAST (phenotype). We then compared the two methods for statistical 'agreement'. A perfect (100%) categorical agreement between genotype and phenotype was observed for gentamicin and meropenem. However, no resistance to meropenem was observed. A high categorical agreement (> 95%) was observed for amoxicillin, cefepime, cefotaxime, ceftazidime, amikacin, and tobramycin. A categorical agreement lower than 95% was observed for amoxicillin/clavulanic acid, piperacillin/tazobactam, and ciprofloxacin. Most discrepancies occurred in isolates with MICs within ± 1 doubling dilution of the breakpoint and 22.73% of the major errors were samples that tested phenotypically susceptible at higher antibiotic exposure and were therefore considered as 'not resistant'. This study shows that WGS can be used as a valuable tool to predict phenotypic resistance against most of the clinically relevant antibiotics used for the treatment of E. coli bloodstream infections.

Molecular characterization of extraintestinal and diarrheagenic Escherichia coli blood isolates.

Pathogenic E. coli strains can be classified into two major groups, based on the presence of specific virulence factors: extraintestinal pathogenic E. coli (ExPEC) and diarrheagenic E. coli (DEC). Several case reports describe that DEC can cause bloodstream infections in some rare cases. This mainly concerns a few specific sequence types that express virulence factors from both ExPEC and DEC. In this study, we retrospectively analysed 234 E. coli blood isolates with whole genome sequencing (WGS). WGS was performed on an Illumina NovaSeq6000. Genotyping was performed using BioNumerics software. The presence of genes was determined with a minimum percentage sequence identity (ID) threshold of 95% and a minimum length for sequence coverage of 95%. Three of the 234 (1.28%) isolates were defined as DEC, 182 (77.78%) as ExPEC, and 49 (20.94%) did not carry pathotype-associated virulence genes. We identified 112 different virulence genes, 48 O-antigens, and 28 H-antigens 82 STs, among the 234 analyzed isolates. ST131 and ST88 were related to healthcare-associated infections. This study provides insight into the prevalence of virulence factors in a large set of E. coli blood isolates from the UZ Brussel. It illustrates high diversity in virulence profiles and highlights the potential of DEC to carry virulence factors associated with extraintestinal infections, making it possible for unusual pathotypes to invade and survive in the bloodstream causing bacteraemia. Diarrheagenic strains causing bacteremia are rare and presently underreported, but modern sequencing techniques will better underscore their importance.

A comparison of E. coli susceptibility for amoxicillin/clavulanic acid according to EUCAST and CLSI guidelines.

In our tertiary care center, the reported susceptibility of E. coli blood isolates to amoxicillin/clavulanic acid exceeded 90% in 2005 and showed a progressive decrease to 50% by 2017. In this study, we investigate whether there is a real increase in resistant E. coli strains or if this apparent decline in reported susceptibility might be attributed to the substitution of CLSI by EUCAST guidelines in 2014. We randomly selected 237 E. coli blood isolates (stored at - 80 °C) from 1985 to 2018 and reassessed their MIC values, applying both the CLSI (fixed ratio of clavulanic acid) and EUCAST guidelines (fixed concentration of clavulanic acid). In parallel, the susceptibility of these isolates was retested by disk diffusion, according to the EUCAST guidelines. Whole genome sequencing was successfully performed on 233 of the 237 isolates. In only 130 of the 237 isolates (55.0%), testing according to the EUCAST and CLSI criteria delivered identical MIC values for amoxicillin/clavulanic acid. In 64 of the 237 isolates (27.0%), the MIC values diverged one dilution; in 38 (16.0%), two dilutions; and in five (2.1%), three dilutions. From these 107 discrepant results, testing according to EUCAST methodology revealed more resistant profiles in 93 E. coli strains (94.1%). Also, phenotypical susceptibility testing according to EUCAST guidelines tends to correlate better with the presence of beta-lactamase genes compared to CLSI testing procedure. This study highlights the low agreement between EUCAST and CLSI methodologies when performing MIC testing of amoxicillin/clavulanic acid. More strains are categorized as resistant when EUCAST guidelines are applied. The low agreement between EUCAST and CLSI was confirmed by WGS, since most of EUCAST resistant/CLSI sensitive isolates harbored beta-lactamase genes.

Sink drains as reservoirs of VIM-2 metallo-ß-lactamase-producing Pseudomonas aeruginosa in a Belgian intensive care unit: relation to patients investigated by whole-genome sequencing.

BACKGROUND: Hospital-acquired infections caused by VIM-encoded metallo-ß-lactamase-positive Pseudomonas aeruginosa are a major problem in intensive care units (ICUs) worldwide. A previous study conducted in the UZ Brussel hospital revealed that sink drains of the ICU were a possible source of various multidrug-resistant pathogenic bacteria. AIM: To investigate the presence and persistence of VIM P. aeruginosa in the sink drains of the four adult ICUs and their role in nosocomial infections, emphasizing sink-to-patient transmission. METHODS: Thirty-six sinks located in the ICUs of the UZ Brussel were sampled and screened for the presence of VIM P. aeruginosa in August and October 2019. Whole-genome sequencing (WGS) was performed on all positive sink drain isolates together with 61 isolates from patients who were retrospectively selected (ICU patients 2019-2020, N = 46; non-ICU patients 2019, N = 6). FINDINGS: Twenty sinks were found positive for P. aeruginosa at both sampling time-points. WGS revealed that the predominating environmental cluster belonged to sequence type ST111. Ten additional STs were identified. VIM-2 was detected among all ST17 (N = 2) and ST111 (N = 14) sink drain isolates. Based on whole-genome multi-locus sequence typing analysis of all genomes, 15 clusters of highly related isolates were identified, of which seven included both sink drain and clinical isolates. CONCLUSION: Our findings confirm that sink drains are a possible source of VIM-2 P. aeruginosa, probably after being contaminated with clinical waste from patients. Patients could be exposed to VIM-2 P. aeruginosa dispersed in their environment because of colonized sink drains.

Serratia marcescens outbreak in a neonatal intensive care unit and the potential of whole-genome sequencing.

BACKGROUND: Serratia marcescens is notorious for its increasing antimicrobial resistance and potential to cause outbreaks in neonatal intensive care units (NICUs). A promising tool in outbreak investigations is whole-genome sequencing (WGS). OBJECTIVES: To describe a S. marcescens outbreak (2018-2019) in an NICU and discuss which infection control measures contributed to containment, addressing the potential of WGS. METHODS: S. marcescens isolates from patients and the environment isolated during the 2018-2019 NICU outbreak were analysed. In comparison, isolates from previous presumed NICU outbreaks and adult blood cultures were included. WGS and whole-genome multi-locus sequence typing analysis were performed. RESULTS: Sixty-three S. marcescens isolates were analysed. The 2018-2019 outbreak was divided into three clusters, including four environmental strains (drains, N=3; baby scale, N=1). The strains differed significantly from those of an NICU outbreak in 2014 and adult blood cultures. Besides standard infection control measures, the siphons were replaced and weekly decontamination was performed with acetic acid 10%. Seven acquired-resistance genes and 29 virulence-associated genes were detected. CONCLUSIONS: It was assumed that both neonates and drains were reservoirs of S. marcescens cross-contamination via the hands of healthcare workers and parents. Initially, standard measures, including hand hygiene, were reinforced. However, definitive containment was achieved only after replacement of the siphons and weekly decontamination with acetic acid. WGS enables faster recognition of an outbreak with accurate mapping of the spread, facilitating the implementation of infection control measures. WGS also provides interesting information about the spread of antibiotic resistance and virulence genes.

Genetic characterization of Shigatoxigenic and enteropathogenic Escherichia coli O80:H2 from diarrhoeic and septicaemic calves and relatedness to human Shigatoxigenic E. coli O80:H2.

AIM: The purpose of this work was to identify and genetically characterize enterohemorrhagic Escherichia coli (EHEC) and enteropathogenic E. coli (EPEC) O80:H2 from diarrhoeic and septicaemic calves in Belgium and to comparing them with human EHEC after whole genome sequencing. METHODS AND RESULTS: Ten EHEC and 21 EPEC O80 identified by PCR between 2009 and 2018 from faeces, intestinal content and a kidney of diarrhoeic or septicaemic calves were genome sequenced and compared to 19 human EHEC identified between 2008 and 2019. They all belonged to the O80:H2 serotype and ST301, harboured the eaeξ gene, and 23 of the 29 EHEC contained the stx2d gene. Phylogenetically, they were distributed in two major sub-lineages: one comprised a majority of bovine EPEC whereas the second one comprised a majority of stx2d bovine and human EHEC. CONCLUSIONS: Not only EPEC but also EHEC O80:H2 are present in diarrhoeic and septicaemic calves in Belgium and are genetically related to human EHEC. SIGNIFICANCE AND IMPACT OF THE STUDY: These findings support the need to assess cattle as potential source of contamination of humans by EHEC O80:H2 and to understand the evolution of bovine and human EHEC and EPEC O80:H2.

Methicillin-resistant Staphylococcus aureus (MRSA) ST398 in pig farms and multispecies farms.

During the last few years, methicillin-resistant Staphylococcus aureus (MRSA) ST398 has been isolated frequently from livestock, especially from pigs and to a lesser extent from cattle and poultry. To gain insight into the distribution of this bacterium in pig farms versus multispecies farms, 30 Belgian farms (10 pig, 10 pig/poultry and 10 pig/cattle farms) were screened for the presence of MRSA. On each farm, 10 nasal swabs were taken from pigs. When present, cattle (n=10) were sampled in the nares and poultry (n=10) in the nares, earlobes and cloaca. A selection of the obtained isolates were further characterized using multilocus sequence typing (MLST), spa typing, SCCmec typing, pulsed field gel electrophoresis (PFGE), multiple-locus variable-number tandem repeat analysis (MLVA) and antimicrobial susceptibility testing. On 26 of 30 farms, MRSA was isolated from pigs. Furthermore, MRSA was also isolated from poultry and cattle on one pig/poultry and five pig/cattle farms, respectively. All tested MRSA isolates belonged to ST398. Eight spa types (t011, t034, t567, t571, t1451, t2974, t3423 and t5943) were detected, among which t011 predominated. SCCmec cassettes type IVa and V were present in 20% and 72% of the isolates, respectively. When combining the results of the two remaining typing methods, PFGE and MLVA, eighteen genotypes were obtained of which one genotype predominated (56% of the positive farms). All MRSA isolates were resistant to tetracycline. Resistance to trimethoprim, aminoglycosides, macrolides, lincosamides, fluoroquinolones and chloramphenicol was also observed. In conclusion, there was no effect of the farm type on the MRSA status of the pigs. A statistically significant difference was observed when comparing the pig/poultry or the pig/cattle MRSA status on the multispecies farms. Additionally, a wide variety of MRSA ST398 strains was found within certain farms when combining different typing methods.

Methicillin-resistant Staphylococcus aureus (MRSA) on the skin of long-term hospitalised horses.

Given the significance of methicillin-resistant Staphylococcus aureus (MRSA) infections for both horses and staff in equine veterinary hospitals, protocols are required to minimise the risk of nosocomial transmission, including the screening of the skin and nasal chambers of equine patients for evidence of infection. The objective of this study was to clarify the potential existence and extent of MRSA on the skin of horses requiring long-term hospitalisation (≥ 6 months). Thirty such horses were sampled at eight different locations on their skin and from their nasal chambers. MRSA was isolated from 12 animals (40%), with all sample sites testing positive on at least one occasion. Organisms were most frequently detected in the nasal chambers (relative sensitivity, 83.3%; 34.5% positive horses; isolation rate 33.3%). Skin presence was found in 30% of animals with the highest isolation rates found at the carpus (16.7%), neck, withers and croup (13.3% each). To achieve a relative screening sensitivity of >90%, at least one skin site was required in addition to nasal sampling. This evidence of skin as well as nasal reservoirs of MRSA in long-term hospitalised horses should facilitate the design of effective screening and containment protocols.

Screening of poultry-pig farms for methicillin-resistant Staphylococcus aureus: sampling methodology and within herd prevalence in broiler flocks and pigs.

Many reports described the prevalence of methicillin-resistant Staphylococcus aureus (MRSA) in different livestock animals from one-species farms. However, in no published reports the prevalence on mixed poultry-pig farms was mentioned, nor the possible relation in MRSA colonization between those two species on one farm, and the possible role of the farmer in the dissemination of MRSA between those two species. Furthermore, no data is available on the optimal sampling site to detect MRSA in broilers. Therefore this study aimed to determine the most suitable sample location in broiler chickens for MRSA and the within flock prevalence of MRSA in various broiler flocks and compared this with the MRSA prevalence in pigs, the colonization of the farmer and the contamination in the barn environment in three mixed poultry-pig farms. MRSA was most frequently isolated from the cloaca and nose shell and to a lesser extent from the skin beneath the wing and the pharynx. The relative sensitivity of the different anatomical sites was, 44.4% for the cloaca, 33.3% for the nose shell, 16.7% for the skin beneath the wing and 5.6% for the pharynx. Based upon these relative sensitivities combining cloaca and nose shell would increase the chance of MRSA detection. A rather low within flock prevalence of MRSA varying between 0% and 28% was detected in broilers, whereas in pigs on the same farms the within herd prevalence varied between 82% and 92%. No MRSA contamination in the direct barn environment of the broilers was found, this in contrast to the environment of the pigs, indicating a relationship between MRSA prevalence and contamination in the environment. Two farmers were continuously colonized, while the third one was only once. In conclusion, a major difference was seen in MRSA occurrence between broilers and pigs from the same farm. This may suggest that broilers are naturally less susceptible to MRSA ST398 colonization than pigs. Conversely, short production time in broilers, vacancy of the barn environment during one week and the higher frequency of disinfection might also explain the lower prevalence in broilers. The farmer may play an important role in the dissemination of MRSA from pigs to poultry, especially in mixed farms where pigs are highly colonized and may act as a reservoir for MRSA ST398 carriage in humans.

Stevioside inhibits atherosclerosis by improving insulin signaling and antioxidant defense in obese insulin-resistant mice.

OBJECTIVE: Stevioside is a non-caloric natural sweetener that does not induce a glycemic response, making it attractive as sweetener to diabetics and others on carbohydrate-controlled diets. Obesity is frequently associated with insulin resistance and increased inflammation and oxidative stress. Therefore, we investigated its effects on insulin resistance, inflammation and oxidative stress related to atherosclerosis in obese insulin-resistant mice. RESEARCH DESIGN: Twelve-week-old mice were treated with stevioside (10 mg kg(-1), n=14) or placebo (n=20) for 12 weeks. RESULTS: Stevioside had no effect on weight and triglycerides, but lowered glucose and insulin. Stevioside treatment improved adipose tissue maturation, and increased glucose transport, insulin signaling and antioxidant defense in white visceral adipose tissues. Together, these increases were associated with a twofold increase of adiponectin. In addition, stevioside reduced plaque volume in the aortic arch by decreasing the macrophage, lipid and oxidized low-density lipoprotein (ox-LDL) content of the plaque. The higher smooth muscle cell-to-macrophage ratio was indicative for a more stable plaque phenotype. The decrease in ox-LDL in the plaque was likely due to an increase in the antioxidant defense in the vascular wall, as evidenced by increased Sod1, Sod2 and Sod3. Circulating adiponectin was associated with improved insulin signaling and antioxidant defense in both the adipose tissue and the aorta of stevioside-treated mice. CONCLUSION: Stevioside treatment was associated with improved insulin signaling and antioxidant defense in both the adipose tissue and the vascular wall, leading to inhibition of atherosclerotic plaque development and inducing plaque stabilization.

Oxidized low-density lipoprotein-induced expression of ABCA1 in blood monocytes precedes coronary atherosclerosis and is associated with plaque complexity in hypercholesterolemic pigs.

BACKGROUND: Elevated oxidized low-density lipoprotein (oxLDL) is associated with atherosclerosis and high cardiovascular risk. Previously, we identified 18 genes in coronary plaque macrophages of hypercholesterolemic pigs that correlated with plaque oxLDL. OBJECTIVE: To determine which of these genes were differentially expressed in blood monocytes and correlated with blood and plaque oxLDL and with plaque complexity. METHODS: RNA expression in monocytes of 27 hypercholesterolemic and 12 control pigs was analyzed with quantitative real-time polymerase chain reaction. RESULTS: Five of 12 genes with detectable expression in monocytes were overexpressed (at P < 0.01 level) in blood monocytes of hypercholesterolemic pigs: ABCA1, SCD, IRF1, SDC2, and TLR2. ABCA1 RNA expression in blood monocytes correlated with blood oxLDL, and its RNA and protein expression was increased prior to atherosclerotic plaque formation. Higher expression of ABCA1 in monocytes was associated with higher plaque complexity and higher plaque oxLDL. Immunostaining of coronary plaques showed the association of ABCA1 with macrophages, lipids, and oxLDL; ABCA1 protein correlated with plaque oxLDL (R(2) = 0.66; P < 0.0001). In THP-1 monocytes, oxLDL induced ABCA1 expression. OxLDL-induced foam cell generation in THP-1 and human monocyte-derived macrophages was associated with a further increase of ABCA1 expression. CONCLUSIONS: The increase of ABCA1 in monocytes in association with blood oxLDL prior to atherosclerotic lesion formation and the association of higher ABCA1 with higher plaque complexity suggests that ABCA1 is an early biomarker of atherosclerosis. Studies in humans are warranted.