Implications of ad-hoc molecular typing for infection control measures in a multi-cluster, multi-phenotypic Serratia marcescens outbreak in a neonatal intensive care unit.

BACKGROUND: Serratia marcescens is known to cause outbreaks in neonatal intensive care units (NICUs). Traditionally epidemiological data, antimicrobial resistance patterns and epidemiological typing have been used to guide infection prevention methods. Whole-genome sequencing (WGS) applications such as core-genome multi-locus sequence typing (cgMLST) applied during an outbreak would potentially yield more information. AIM: To use cgMLST to acquire detailed information on the source and spread of bacteria, enabling more efficient control measures during an S. marcescens outbreak at a NICU. METHODS: Neonates admitted to the NICU of the Leiden University Medical Center (LUMC) during an outbreak between September 2023 and January 2024, with S. marcescens being cultured, were included. Environmental samples were taken to search for a common source, antibiotic susceptibility testing was performed, and antimicrobial resistance genes were analysed. FINDINGS: S. marcescens strains from 17 of the 20 positive patients were available for molecular typing. The cgMLST scheme revealed five different complex types consisting of four separate clusters. Multiple clusters made an unidentified persistent environmental source as cause of the outbreak less likely, leading to a quick downscaling of infection prevention measures. Differences were shown in aminoglycoside resistance patterns of isolates within the same complex types and patients. CONCLUSION: The use of ad-hoc cgMLST provided timely data for rational decision-making during an S. marcescens outbreak at the NICU. Antibiotic phenotyping alone was found not to be suitable for studying clonal spread during this outbreak with S. marcescens.

Influence of transition from open bay units to single room units in a neonatal intensive care unit on hospital transmission of multi-drug-resistant Enterobacterales.

BACKGROUND: It was shown previously that changing the design of a hospital neonatal intensive care unit (NICU) from open bay units (OBUs) to single room units (SRUs) was not associated with a reduction in Gram-negative multi-drug-resistant organism (MDRO) colonization rates. It was therefore hypothesized that colonization mainly occurs vertically, or through parents and healthcare workers, and not through environmental factors, and that transition to SRUs would not decrease the number of clusters of MDROs with an epidemiological link. To investigate this, core-genome multi-locus sequence typing (cgMLST) was applied on MDROs cultured from infants at the study hospital. METHODS: This retrospective cohort study included all infants carrying MDROs admitted to the NICU of a tertiary care academic hospital 2 years prior to the transition from OBUs to SRUs in May 2017, and 1.5 years after the transition (2018-2020). RESULTS: In total, 55 infants were diagnosed with MDRO carriership. Isolates were available from 49 infants for cgMLST. In the OBU period, one cluster involving four of 20 (20%) infants was identified, and in the SRU period, four clusters involving nine of 29 (31%) infants were identified. It was possible to make an epidemiological link in all four SRU MDRO clusters, but this was not possible for the OBU cluster. In the latter case, transmission from an environmental source on the ward seemed likely. CONCLUSION: After transition to SRUs, there was no decrease in the number of clusters of MDROs with an epidemiological link, suggesting that nursing infants in an NICU with an SRU design is not, in itself, protective against the acquisition of MDROs.

Clinical performance of two new, fully integrated molecular platforms used for HIV-1, HBV and HCV viral load analysis, the NeuMoDx 288 and the Alinity m.

BACKGROUND: Viral load (VL) determination in patients with human immunodeficiency virus type 1 (HIV-1), hepatitis B virus (HBV) and hepatitis C virus (HCV) is essential for proper patient management and follow-up. New molecular platforms have been developed to fully automate these diagnostic assays. OBJECTIVE: Evaluation of the clinical performance of HIV-1, HBV and HCV VL assays on the Alinity m (Abbott) and NeuMoDx (Qiagen) molecular platforms. METHOD: Test panels of the three viruses have been compiled of 100 plasma and/or serum samples per target containing non-detectable, non-quantifiable and quantifiable VLs. All samples were retrospectively tested on the Alinity m and NeuMoDx platforms according to manufacturers' instructions. RESULTS: A total of 74, 86 and 66 samples with valid results for both platforms were included in the HIV-1, HBV and HCV analysis respectively. Overall qualitative agreement of the assays on both platforms was 78% for HIV-1, 93% for HBV and 100% for HCV. Quantitative agreement (less than 0.5 log difference) was shown to be 68% for HIV-1, 68% for HBV and 94% for HCV. CONCLUSION: The Alinity m and NeuMoDx HCV assay have a comparable performance. Quantification differences in the HIV-1 assay were mostly apparent in the lower VLs and under-quantification of the NeuMoDx HBV assay was observed.

Long-term outcomes after close rectal dissection and total mesorectal excision in ileal pouch-anal anastomosis for ulcerative colitis.

BACKGROUND: During ileal pouch-anal anastomosis (IPAA) surgery for ulcerative colitis (UC), rectal dissection can be performed via close rectal dissection (CRD) or in a total mesorectal excision plane (TME). Although CRD should protect autonomic nerve function, this technique may be more challenging than TME. The aim of this study was to compare long-term outcomes of patients undergoing CRD and TME. METHODS: This single-centre retrospective cohort study included consecutive patients who underwent IPAA surgery for UC between January 2002 and October 2017. Primary outcomes were chronic pouch failure (PF) among patients who underwent CRD and TME and the association between CRD and developing chronic PF. Chronic PF was defined as a pouch-related complication occurring ≥ 3 months after primary IPAA surgery requiring redo pouch surgery, pouch excision or permanent defunctioning ileostomy. Secondary outcomes were risk factors and causes for chronic PF. Pouch function and quality of life were assessed via the Pouch dysfunction score and Cleveland global quality of life score. RESULTS: Out of 289 patients (155 males, median age 37 years [interquartile range 26.5-45.5 years]), 128 underwent CRD. There was a shorter median postoperative follow-up for CRD patients than for TME patients (3.7 vs 10.9 years, p < 0.01). Chronic PF occurred in 6 (4.7%) CRD patients and 20 (12.4%) TME patients. The failure-free pouch survival rate 3 years after IPAA surgery was comparable among CRD and TME patients (96.1% vs. 93.5%, p = 0.5). CRD was a no predictor for developing chronic PF on univariate analyses (HR 0.7 CI-95 0.3-2.0, p = 0.54). A lower proportion of CRD patients developed chronic PF due to a septic cause (1% vs 6%, p = 0.03). CONCLUSIONS: Although differences in chronic PF among CRD and TME patients were not observed, a trend toward TME patients developing chronic pelvic sepsis was detected. Surgeons may consider performing CRD during IPAA surgery for UC.

Evaluation of the sample-to-result, random access NeuMoDx platform for viral load testing of Cytomegalovirus and Epstein Barr virus in clinical specimens.

BACKGROUND: The detection and follow up of cytomegalovirus (CMV) and Epstein-Barr virus (EBV) viral loads (VL) are crucial in the management of immunocompromised patients. Recently, molecular CE-IVD assays for detection and quantification of CMV and EBV have been launched for use on the random-access and sample-to-result NeuMoDx 96 and 288 platforms (Qiagen). OBJECTIVE: Evaluating the qualitative and quantitative performance of the NeuMoDx CMV and EBV assays in clinical specimens compared to a lab developed tests (LDT) and the CE-IVD assays on the Abbott m2000 system. METHOD: Both a prospective and a retrospective panel, compiled of non-detectable (ND), non-quantifiable (NQ) and quantifiable VLs in plasma samples have been evaluated for both CMV and EBV: NeuMoDx versus LDT and NeuMoDx versus Abbott m2000. Quantitative agreement was determined for samples with a quantifiable VL on both systems. RESULTS: Qualitative and quantitative agreement between the NeuMoDx and LUMC's LDT CMV assays was 88%. Qualitative agreement between the NeuMoDx and Abbott m2000 CMV assays was 92% and quantitative agreement was 87%. Qualitative and quantitative agreement between the NeuMoDx and the LDT EBV assays was 87%. Qualitative agreement between the NeuMoDx and Abbott m2000 EBV assays was 91% and quantitative agreement was 0%. CONCLUSION: These data show that the NeuMoDx assays are suitable for both detection and quantification of CMV and EBV in a medium- to high throughput diagnostic setting, but that differences in sensitivity and quantification (for EBV, NeuMoDx versus Abbott m2000) warrant an extensive transition period when using the respective assays for following VL in patient samples.

The spectrum of animal related injuries managed at a major trauma centre in South Africa.

BACKGROUND: Humans come into contact and interact with an array of animals in a number of areas and environments. We set out to review our experience with animal-related injuries in Pietermaritzburg, KwaZulu-Natal, South Africa. METHOD: All patients who sustained an injury secondary to an interaction with an animal in the period December 2012-December 2017 were identified from the Hybrid Electronic Medical Registry (HEMR). RESULTS: There were 104 patients in the study sample. The mean age of patients in the study was 32.8 years, with a range from 1 to 76 years old. 75% (n = 78) were male and 25% (n = 26) female. Out of the 104 animal-related injuries, 67 were blunt trauma, 39 penetrating trauma and 3 a combination of blunt and penetrating trauma. The species causing trauma included dogs (53), horses (29), cows (18), buffalo (1), warthog (1), impala (1) and a single goat (1). The median time from injury to hospitalisation was 46.62 hours (range from 0 to 504 hours). Injuries occurred to the head (n = 32), face (n = 9), neck (n = 32), abdomen (n = 22), urogenital system (n = 6), upper limb (n = 39) and lower limb (n = 39). The Injury Severity Score (ISS) mean for the patients was 8.16, the range 1-4, the median 9 and the standard deviation 6.88. In 49 patients the treatment was non-operative. In the remaining 55 patients, a total of 68 operative procedures were required. Operations included wound debridement/surgical washout (n = 38), laparotomy (n = 9), arterial repair/ligation (n = 8), skin graft (n = 4), craniotomy (n = 5), fasciotomy (n = 2), amputation (n = 1), and placement of an ICP monitor (n = 1). 49 of these operations were for patients with dog bite injuries. The mean hospital stay was 0.13 days with a range of 0-4 days. Four patients were admitted to the Intensive Care Unit (ICU) and two patients died. CONCLUSION: Human interactions with animals may result in injuries which require surgical treatment. The most common animal injury is a dog bite but in the case of the larger domestic farm animals, blunt force type injuries and goring can result in significant injuries which require complex surgical interventions.

Multiplex real-time PCR for diagnosing malaria in a non-endemic setting: a prospective comparison to conventional methods.

Almost a decade ago our diagnostic laboratory implemented an in-house real-time PCR for the detection of Plasmodium DNA to diagnose malaria in parallel with conventional diagnostics, i.e., microscopy (thick and thin smears), quantitative buffy coat microscopy (QBC), and a rapid diagnostic test (RDT). Here we report our experiences and make a comparison between the different diagnostic procedures used in this non-endemic setting. All patients during the period February 2009-December 2017 suspected of malaria were prospectively tested at the moment of sample collection. Both PCR and conventional malaria diagnostics were carried out on a total of 839 specimens from 825 patients. In addition, three Plasmodium falciparum (Pf) patients were closely followed by real-time PCR and microscopy after treatment. Overall, 56 samples (55 patients) tested positive by real-time PCR, of which six were missed by microscopy and seven by QBC. RDT showed fairly good results in detecting Pf, whereas specificity was not optimal. RDT failed to detect 10 of 17 non-Pf PCR positive specimens. One Plasmodium malariae patient would have been missed if only conventional diagnostic tests had been used. The high sensitivity of the PCR was confirmed by the number of PCR positive, microscopy negative post-treatment samples. In conclusion, within our routine diagnostic setting, malaria real-time PCR not only showed a high level of agreement with the conventional methods used, but also showed higher sensitivity and better specificity. Still, for complete replacement of the conventional procedures in a non-endemic setting, the time-to-results of the real-time PCR is currently too long.

PCR assays for detection of human astroviruses: In silico evaluation and design, and in vitro application to samples collected from patients in the Netherlands.

BACKGROUND: Human astroviruses (HAstV) comprise three phylogenetically compact and non-adjacent groups of species including classical HAstV (HAstV-C) and the novel ones (HAstV-VA/HMO and HAstV-MLB). Of these, HAstV-C is known to be responsible for gastroenteritis while the novel HAstV are associated with cases of neurological disorders. Accurate detection of all known variants by (real-time) PCR is challenging because of the high intra- and intergroup genetic divergence of HAstV. OBJECTIVES: To evaluate published HAstV PCR assays in silico, design de novo real-time PCR assays that can detect and discriminate three groups of HAstV, and apply those to patient samples to analyse the prevalence of HAstV in stool and cerebrospinal fluid (CSF) specimens. STUDY DESIGN: In silico evaluation of published PCR assays and design of real-time PCR assays for detection of different subsets of HAstV was conducted within a common computational framework that used all astrovirus full genome sequences from GenBank. The newly designed real-time PCR assays were evaluated in vitro and applied to faecal samples (collected in January-May 2016) and cerebrospinal fluid specimens (2010-2016) from patients in the Netherlands. RESULTS: Quantitative in silico evaluation of published PCRs is provided. The newly designed real-time PCR assays can reliably assign all available HAstV genome sequences to one of the three phylogenetic groups in silico, and differentiate among HAstV-specific controls in vitro. A total of 556 samples were tested using these PCR assays. Fourteen fecal samples (2.5%) tested positive for HAstV, 3 of which could be identified as the novel HAstV-MLB variants. No novel HAstV were found in CSF specimens. CONCLUSION: Newly designed real-time PCR assays with improved detection of all known HAstV allowed the first-time identification of novel astroviruses from stool samples in the Netherlands.

Added value of multiplex Luminex Gastrointestinal Pathogen Panel (xTAG® GPP) testing in the diagnosis of infectious gastroenteritis.

The Luminex Gastrointestinal Pathogen Panel (xTAG(®) GPP) detects in one assay the most common gastroenteritis-causing pathogens and toxins, namely adenovirus 40/41, norovirus genogroup (NG) I/II, rotavirus A, Clostridium difficile toxin A/B, Campylobacter sp., Escherichia coli O157, Enterotoxigenic E. coli heat-labile enterotoxin/heat-stable enterotoxin, Salmonella sp., Shiga-toxin producing E. coli, Shiga-like toxin (Stx)1/2, Shigella sp., Vibrio cholerae, Yersinia enterocolitica, Cryptosporidium sp., Entamoeba histolytica and Giardia sp. In this study, we compared the results that were obtained by testing 393 faecal samples, collected during November and December 2011 at our laboratory, using the xTAG(®) GPP assay with the results of the routine diagnostic procedure. This procedure includes culture for bacteria and real-time PCR for viruses and parasites, but only if the test was requested by the clinician. If the clinician did not request the test for an xTAG(®) GPP-positive target, real-time PCR assays were used to confirm xTAG(®) GPP positivity. Discrepant results were also tested with real-time PCR assays. A total of 83 targets were detected in 76 samples using xTAG(®) GPP. The xTAG(®) GPP assay detected 43 additional positives compared with the routine diagnostic procedure, of which 11 targets could not be confirmed by real-time PCR. The non-confirmed targets were Campylobacter (one sample), Salmonella (four samples), Shigella (one sample) and E. histolytica (five samples). The xTAG(®) GPP was shown to be a convenient and sensitive assay for detection of 15 major gastrointestinal pathogens in a single molecular test, but for detection of E. histolytica and Salmonella, a confirmatory assay is indicated.

Characterization of fluoroquinolone and cephalosporin resistance mechanisms in Enterobacteriaceae isolated in a Dutch teaching hospital reveals the presence of an Escherichia coli ST131 clone with a specific mutation in parE.

OBJECTIVES: To characterize the mechanisms of fluoroquinolone and cephalosporin resistance in Enterobacteriaceae from a Dutch teaching hospital in 2008. METHODS: We sequenced gyrA, gyrB, parC and parE. The presence of plasmid-encoded genes qnrA, qnrB, qnrS, aac(6')-Ib, qepA, bla(TEM), bla(SHV,) bla(OXA), bla(CTX-M) and bla(AmpC) was studied by PCR. Escherichia coli isolates were further characterized by AFLP and multilocus sequence typing (MLST). RESULTS: In total, 49 E. coli, 16 Klebsiella pneumoniae and 3 Enterobacter cloacae isolates were investigated. Mutations in gyrA were found in all E. coli isolates. Forty-five (92%) E. coli isolates carried at least one point mutation in parC. Most E. coli isolates (59%) also carried mutations in parE, of which I529L was the most prevalent. I529L was unequivocally associated with E. coli sequence type (ST) 131. This single-nucleotide polymorphism (SNP) was later also found in eight out of nine ST131 strains from another collection. Twenty-nine E. coli isolates carried extended-spectrum ß-lactamase (ESBL) genes, predominantly bla(CTX-M-15). In E. coli, aac(6')-Ib-cr was the predominant plasmid-mediated resistance mechanism, whereas in K. pneumoniae qnr genes were found mostly. In K. pneumoniae isolates, qnr and aac(6')-Ib-cr co-occurred with ESBL genes (n = 13; bla(CTX-M) and bla(SHV)) and/or bla(AmpC) (n = 3; bla(DHA-1)). CONCLUSIONS: E. coli ST131 was the predominant clone, which accumulated a high number of chromosomal mutations. The I529L SNP in parE was a signature of most, but not all, ST131 strains. In contrast to E. coli, fluoroquinolone resistance mechanisms were predominantly plasmid-encoded in K. pneumoniae.

Potential influence of more-sensitive HIV-1 load detection by the new Roche Cobas AmpliPrep/Cobas TaqMan version 2.0 assay on clinical management of HIV-positive pregnant women.

With the introduction of the new Roche Cobas AmpliPrep/Cobas TaqMan version 2.0 assay, HIV-1 viral loads will be detected more frequently during the peripartum period in pregnant HIV-positive women. The implications for the clinical management of these patients are discussed in this paper.

Cryptococcal meningitis in an HIV negative patient with systemic sarcoidosis.

A case of Cryptococcus neoformans meningitis is described in an HIV negative patient with undiagnosed systemic sarcoidosis. The patient presented with signs of meningitis together with generalised lymphadenopathy and hepatosplenomegaly. Cryptococcal meningitis was diagnosed on lumbar puncture. She was treated with intravenous amphotericin B but died within two weeks of admission. Necropsy revealed lesions in the lungs, liver, spleen, lymph nodes, small intestine, and bone marrow consistent with sarcoidosis. Microscopically the lesions contained non-caseating epithelioid cell granulomas typical of sarcoidosis. No Schaumann or Hamazaki-Wesenberg bodies were identified. Cryptococcus neoformans meningitis is generally associated with immunosuppressive disorders. As T cell abnormalities have been described in sarcoidosis, this could have been a case of opportunistic infection. Although rare, sarcoidosis merits consideration in patients with cryptococcal disease in the absence of HIV infection.

Some small prostate cancers are nondiploid by nuclear image analysis: correlation of deoxyribonucleic acid ploidy status and pathological features.

The biological behavior of a prostate cancer can be predicted to some degree by the volume and extent (stage) of the tumor, and its histological grade. The deoxyribonucleic acid (DNA) ploidy status has been reported by some to be another independent prognostic factor for localized prostate cancer. We determined the DNA ploidy value of each individual focus of cancer in radical prostatectomy specimens using nuclear image analysis (CAS 200 system). Ploidy results were correlated with the volume, Gleason grade and zone of origin (transition zone or peripheral zone) of each tumor, and with the presence of extracapsular extension or seminal vesicle invasion. There were 141 separate cancers in 68 patients (mean 2.1 per prostate): 9 clinical stage A1, 22 stage A2, 23 stage B1 and 14 stage B2. DNA ploidy correlated significantly (p < 0.0001) with volume, grade, extraprostatic spread and zone of origin. Remarkably, some small cancers (1 cc or less) were nondiploid (3 as small as 0.03 cc). Overall, 15% of cancers 0.01 to 0.1 cc and 31% of those 0.11 to 1.0 cc in volume were nondiploid. Of 101 cancers confined to the prostate 76% were diploid, compared to only 13% of those with extraprostatic spread. Most cancers of transition zone origin (86%) were diploid, compared to only 49% of peripheral zone cancers, and ploidy and volume relationships were significantly different for peripheral zone cancers compared to transition zone cancers. All small nondiploid cancers arose in the peripheral zone, while in the transition zone the smallest nondiploid cancer was 1.17 cc. We conclude that prostate cancers that are nondiploid are highly likely to have adverse pathological features. Some small prostate cancers contain a nondiploid cell population and these cancers arise predominantly within the peripheral zone of the prostate. Ploidy and volume relationships provide further support for the hypothesis that there is a difference in malignant potential between cancers of peripheral zone and transition zone origin.

[Coping strategies of mothers and fathers with a first- or second-born mentally handicapped child]. / Bewältigungsstrategien von Müttern und Vätern mit einem erst- oder zweitgeborenen geistig behinderten Kind.

In 25 families with two children and one child with mental retardation, differences in coping between mothers and fathers were studied, taking into consideration the ordinal position of the handicapped child. Mothers showed more emotional stress, more self-criticism, searched more for social support and experienced more "up and down" in the process of adaptation. If the first child was handicapped mothers coped more by "mastery" than mothers of a second born handicapped child and more by "expression" than fathers.

Ultrasonic detection of non-palpable seminal vesicle invasion: a clinicopathological study.

In an effort to identify reliable criteria for detecting seminal vesicle invasion (SVI) with transrectal ultrasonography (TRUS) in patients with clinically localised prostate cancer, we reviewed the pre-operative sonograms in 230 patients who underwent radical retropubic prostatectomy; 49 patients (21%) had pathologically confirmed SVI. Conventional sonographic criteria for SVI (asymmetry, distension, atrophy, abnormal echogenicity and irregularity in outline) were present in 58 patients, but only 16 (28%) had pathologically confirmed SVI. On the basis of the results of a preliminary comparison of radical prostatectomy specimens and TRUS, we had revised our criteria for the recognition of SVI: (1) a hypoechoic lesion at the base of the prostate (within 10 mm of the seminal vesicle); (2) an "adhesion sign" resulting from the loss of the echo reflections from the normal fat plane between the prostate and the seminal vesicle; (3) "posterior convexity" of the seminal vesicles. When we reviewed the 230 sonograms retrospectively, we found a hypoechoic tumour at the base in 70 patients, of whom 37 had SVI (positive predictive value (PPV) 53%). An adhesion sign was found in 16 patients, 12 of whom had SVI (PPV 75%). Posterior convexity was present in 4 patients, all of whom had SVI. If any one of our sonographic signs was present, the overall accuracy (83%), sensitivity (90%) and positive predictive value (51%) were significantly better than with any one of the conventional criteria. Patients with SVI were also more likely to have a high serum prostate specific antigen (PSA) level. The PPV for SVI of a PSA level > or = 10 ng/ml was 38%. If the PSA was > 10 ng/ml and TRUS was positive (> or = 1 of our sonographic criteria), 16 (62%) of 26 patients had SVI. If the PSA was < 10 ng/ml and TRUS was negative, only 3 (3%) of 86 patients had SVI. It was concluded that the conventional criteria for detecting SVI on ultrasonography are not accurate in patients with early stage prostate cancer. There are, however, reliable criteria that predict SVI with reasonable accuracy and these criteria, combined with the serum PSA levels, can stratify patients into those with a low risk and those with a high risk of SVI.