In vivo selection of carbapenem resistance during persistent Klebsiella pneumoniae sequence type 395 bloodstream infection due to OmpK36 deletion.

Non-carbapenemase-producing carbapenem-resistant Enterobacterales (non-CP CRE) may be associated with a grave outcome. The common underlying mechanism is beta-lactamases and mutations in outer membrane porins. We report a case of a deep-seated infection caused by Klebsiella pneumoniae ST395 not amenable to source control, involving recurrent bloodstream infection, resulting in in vivo selection of carbapenem resistance under therapy. Three consecutive K. pneumoniae blood isolates were studied using short- and long-read sequencing. The genomes were subject to resistome and virulome, phylogenetic, and plasmid analyses. ompK36 porins were analyzed at the nucleotide and amino acid levels. Genomes were compared to 297 public ST395 K. pneumoniae genomes using cgMLST, resistome, and porin analyses and the EuSCAPE project. Relevant ompK36 and micF sequences were extracted and analyzed as above. The three sequential K. pneumoniae blood isolates belonged to the same clone. Subsequent CR isolates revealed a new large deletion of the ompK36 gene also involving the upstream region (deletion of micF). Comparison with public ST395 genomes revealed the study isolates belonged to clade B, representing a separate clone. N-terminal large ompK36 truncations were uncommon in both public data sets. In vivo selection of non-CP CRE K. pneumoniae could have substantial clinical implications. Such selection should be scrutinized through repeated cultures and frequent susceptibility testing during antimicrobial treatment, especially in the context of persistent or recurrent bloodstream infections and when adequate source control cannot be achieved. The occurrence of an unusually large deletion involving the ompK36 locus and upstream micF should be further studied.

Invasive infections caused by the recently described species Enterococcus innesii.

E. innesii is a recently described Enterococcus species which may be difficult to differentiate from the more common E. casseliflavus. We present the first clinical report of invasive E. innesii infection, featuring two cases of biliary sepsis. Whole genome sequencing confirmed the taxonomic assignment and the presence of vanC-4. Analysis of public genomes identified 13 deposited E. innesii and 13 deposited E. casselifalvus/E.gallinarum genomes which could be reassigned as E. innesii. Improved laboratory diagnosis of E. innesii is expected to generate additional data concerning its clinical relevance and support the future diagnosis and treatment of this uncommon pathogen.

Metagenomic sequencing for investigation of a national keratoconjunctivitis outbreak, Israel, 2022.

BackgroundEpidemics of keratoconjunctivitis may involve various aetiological agents. Microsporidia are an uncommon difficult-to-diagnose cause of such outbreaks.AimDuring the third quarter of 2022, a keratoconjunctivitis outbreak was reported across Israel, related to common water exposure to the Sea of Galilee. We report a comprehensive diagnostic approach that identified Vittaforma corneae as the aetiology, serving as proof of concept for using real-time metagenomics for outbreak investigation.MethodsCorneal scraping samples from a clinical case were subjected to standard microbiological testing. Samples were tested by calcofluor white staining and metagenomic short-read sequencing. We analysed the metagenome for taxonomical assignment and isolation of metagenome-assembled genome (MAG). Targets for a novel PCR were identified, and the assay was applied to clinical and environmental samples and confirmed by long-read metagenomic sequencing.ResultsFluorescent microscopy was suggestive of microsporidiosis. The most abundant species (96.5%) on metagenomics analysis was V. corneae. Annotation of the MAG confirmed the species assignment. A unique PCR target in the microsporidian rRNA gene was identified and validated against the clinical sample. The assay and metagenomic sequencing confirmed V. corneae in an environmental sludge sample collected at the exposure site.ConclusionsThe real-time utilisation of metagenomics allowed species detection and development of diagnostic tools, which aided in outbreak source tracking and can be applied for future cases. Metagenomics allows a fully culture-independent investigation and is an important modality for public health microbiology.

False-positive galactomannan antigen testing in pulmonary nocardiosis.

Early diagnosis of invasive aspergillosis (IA) is facilitated by detection of galactomannan (GM) in serum and bronchoalveolar lavage fluid (BALF) using an enzyme-linked immunosorbent assay (ELISA). Although accurate, false positive results have been reported with these tests in numerous contexts. We report for the first time the occurrence of false positive GM ELISA due to nocardiosis, initially in a clinical sample of BALF from a patient with pulmonary nocardiosis, and subsequently corroborated by in vitro reactivity of 26% of tested isolates. Since patients at risk for IA are also at risk for nocardiosis, this finding has important clinical implications. LAY SUMMARY: Early diagnosis of aspergillosis has been facilitated by the routine use of antibody-based detection of galactomannan in various bodily fluids. We report for the first time the occurrence of false positive results of this assay in the context of nocardiosis.

Tickborne Relapsing Fever, Jerusalem, Israel, 2004-2018.

To compare tickborne relapsing fever (TBRF) in children and adults in Jerusalem, Israel, we collected data from the medical records of all 92 patients with TBRF during 2004-2018. The 30 children with TBRF had more episodes of fever and lower inflammatory markers than adult patients.

Gram-negative Bacteremia in Children With Hematologic Malignancies and Following Hematopoietic Stem Cell Transplantation: Epidemiology, Resistance, and Outcome.

Gram-negative rod (GNR) infections adversely affect the outcome of patients with malignancies and following hematopoietic stem cell transplantation (HSCT). This retrospective observational study aimed to describe the epidemiology, outcome, and resistance patterns of GNR bacteremia in children with hematologic malignancies (HM) and after HSCT during the period spanning from 2010 to 2014 in a tertiary children's hospital. A total of 270 children were included in the analysis; 65 (24%) developed 85 episodes of GNR bacteremia; the rate was 36/122 (29.5%) in post-HSCT and 29/178 (16.3%) in HM patients (P<0.05). Overall, 10% of the GNRs were carbapenem resistant. In multivariate analysis, prolonged neutropenia (≥7 d; odds ratio: 19.5, 95% confidence interval: 2.6-148.4) and total hospitalization for a duration of >30 days in the last 3 months (odds ratio: 17.5, 95% confidence interval: 1.4-224.4) were associated with carbapenem-resistant GNR bacteremia. Thirty-day mortality following GNR bacteremia was 0% in HM and 7/52 episodes (13.5%) in HSCT patients (P<0.05). Carbapenem-resistant versus carbapenem-sensitive bacteremia was associated with longer duration of bacteremia (mean: 3.8 vs. 1.7 d), higher risk for intensive care unit hospitalization (44.4% vs. 10.1%), and higher mortality rate (33% vs. 5.8%) (P<0.05). To summarize, GNR bacteremia was frequent, especially in post-HSCT children. Carbapenem resistance adversely affects patients' outcome, increasing morbidity and mortality. Empirical antibiotic therapy must be adjusted to the local resistance patterns.

Infections caused by Fusobacterium in children: a 14-year single-center experience.

PURPOSE: This study aimed at reviewing our experience with infections caused by Fusobacterium in children. METHODS: A retrospective analysis of medical records of children admitted to Hadassah-Hebrew University Medical Center from 2000 to 2013, in whom Fusobacterium spp. was identified in any specimen. RESULTS: A total of 22 patients (males = 12) at a mean ± SE age of 5 ± 1 (range 1-17) years, were identified. The most common complication was abscess formation (n = 11, 50 %). Eight children (36.4 %) had intracranial complications, including brain abscess (n = 4), meningitis (n = 4) and cerebral sinus vein thrombosis (CSVT, n = 5). Seventeen children (77 %) had bacteremia. Primary site of infection was otogenic (n = 9), oropharyngeal (n = 7), respiratory (n = 2), sinuses (n = 2), intra-abdominal (n = 1) and mucositis (n = 1). Fourteen cases were caused by Fusobacterium necrophorum, including four cases with CSVT, 7/8 cases of mastoiditis, four of them with subperiosteal abscess formation; all four cases with meningitis and two brain abscesses. Fifteen (68 %) patients required surgical intervention and 3 (14 %) received anti-coagulation therapy. Excluding one patient with overwhelming sepsis with fatal outcome, all patients recovered. CONCLUSIONS: Fusobacterium infections in children can cause a diverse spectrum of disease and is associated with high rates of abscess formation and intracranial complications. Although Fusobacterium nucleatum is abundant in the oral cavity, F. necrophorum is the main pathogen that causes severe infections in healthy children.

Enterococcal Central Nervous System Infections in Children: A 22 Years' Experience in a Tertiary Center and Review of the Literature.

BACKGROUND: Enterococcal meningitis in children is rare, and its clinical presentation, laboratory characteristics and outcomes are not well defined. METHODS: We conducted a retrospective analysis of Enterococcal meningitis cases during 2002-2023 at our tertiary center. RESULTS: We identified 10 cases in children aged 2 weeks to 15 years (median age: 8 months). Seven children were males and 9 had comorbidities, including a ventriculoperitoneal shunt in 5 children. All children with shunt infections presented with nonspecific signs and symptoms. While 8 children presented with fever, only 3 had signs of meningeal irritation and altered consciousness. Cerebrospinal fluid pleocytosis was evident in almost all children with a median of 173 cells/mL. Nine cases were due to Enterococcus faecalis, and 1 case was due to E. faecium. All 5 children with ventriculoperitoneal shunt underwent shunt removal and replacement. All children recovered without documented sequelae. CONCLUSIONS: Enterococcal meningitis is rare, especially in healthy neonates. It typically occurs following neurosurgical interventions and may only present with fever and shunt malfunction, without overt meningeal signs and with mild inflammation. The prognosis is favorable.

Helicobacter cinaedi Bacteremia in Children: A Case Report and Literature Review.

Helicobacter cinaedi is known to cause invasive infections in immunocompromised adults. Here we report the first case of H. cinaedi bacteremia in a child with nephrotic syndrome. The patient presented with a mild transient febrile illness that resolved spontaneously. We discuss the diagnostic challenges associated with this case and the microbiologic approach, including genomic analysis. Furthermore, we review the current case together with all previous pediatric cases (n = 6). Notably, all cases involved neonates or otherwise immunocompromised individuals and were characterized by severe disease with complicated infections (eg, meningitis, cholangitis and arthritis). H. cinaedi bacteremia in children is associated with a wide spectrum of clinical presentations ranging from mild to life-threatening conditions. This bacterium may be difficult to diagnose and require specialized methods.

Invasive Fungal Infections in Children with Acute Leukemia: Epidemiology, Risk Factors, and Outcome.

Invasive fungal infections (IFI) cause morbidity and mortality in children with acute leukemia (AL). We retrospectively collected data on febrile neutropenic episodes (FNE) in AL children (2016-2021) and assessed factors associated with proven/probable IFI. Ninety-three children developed 339 FNE. Seventeen (18.3%) children developed 19 proven/probable IFI (11 yeast; eight molds). The proven/probable yeast IFI rate was 6/52 (11.5%) in children who belong to the high risk for IFI category (HR-IFI-AL: high-risk acute lymphocytic leukemia (ALL), acute myeloid leukemia, relapse); and 5/41 (12.2%) in the non-HR-IFI-AL category (standard/intermediate risk ALL). The proven/probable mold IFI rate was 7/52 (13.5%) in HR-IFI-AL children and 1/41 (2.4%) in the non-HR-IFI-AL category. In the multivariable analysis, underlying genetic syndrome, oral mucositis, and older age were significantly associated with proven/probable IFI, while a longer time since AL diagnosis was protective. Two of 13 (15.4%) HR-IFI-AL children died because of IFI. The elevated risks of proven/probable mold IFI and the associated mortality in HR-IFI-AL children, and high risk of invasive candidiasis in the non-HR-IFI-AL group, emphasize the need for the close monitoring of local epidemiology and the adjustment of practices accordingly.

A 14-Year Cohort of Candidemia in the Pediatric Population in a Tertiary Center in Jerusalem: Clinical Characteristics, Antifungal Susceptibility, and Risk Factors for Mortality.

Candida spp. can cause bloodstream infection and is associated with significant mortality. The proportion of fluconazole-resistant Candida non-albicans has increased over the years, and empirical fluconazole maybe inappropriate. In this retrospective study, we analyzed clinical characteristics, antifungal resistance patterns, and mortality in children with candidemia treated at a tertiary medical center in Jerusalem between 2009 and 2022. A total of 122 children developed 127 candidemia episodes with 132 Candida isolates. Half the episodes occurred in immunocompromised children. Septic shock was present in 27 (21.3%). Candida non-albicans was responsible for 71/132 (56.5%) episodes; 16/132 (12.1%) of isolates were fluconazole-resistant. The rate of Candida non-albicans was significantly higher in fluconazole-resistant episodes (90 vs. 50.5%, p = 0.02). Prolonged severe neutropenia and previous fluconazole exposure were more frequent in fluconazole-resistant episodes. Thirty-day mortality was 25 (19.7%). Greater mortality, as shown by multivariate analysis, was associated with candidemia contracted in the pediatric intensive care unit (PICU), previous use of azoles or carbapenems, and in the presence of shock. In conclusion, mortality rates in our study were higher than those previously reported. In suspected infection associated with factors which we found to increase the probability of mortality-PICU admission, shock, and earlier azole or carbapenems exposure-empirical antifungals should be considered.

KPC-9, a novel carbapenemase from clinical specimens in Israel.

A bla(KPC-9) carbapenemase variant was discovered in isolates of Klebsiella pneumoniae and Escherichia coli from a single patient. It differed from bla(KPC-3) by one amino acid substitution (Val239Ala). The K. pneumoniae isolate was typed as ST258, as was the epidemic Israeli KPC-3 clone. bla(KPC-9) was found on a plasmid indistinguishable from pKpQIL that carries bla(KPC-3) in the epidemic clone. Compared to KPC-3, KPC-9 conferred less resistance to carbapenems and higher resistance to ceftazidime.

Comparison of two carbapenem-resistant Klebsiella pneumoniae clones: from a contained outbreak in a paediatric population and from a national epidemic.

OBJECTIVES: A refractory epidemic of carbapenem-resistant Klebsiella pneumoniae (CRKP) emerged in the adult population at our hospital in 2005, as in most Israeli hospitals. Contemporaneously, a different clone of CRKP caused an easily contained outbreak in a paediatric long-term care facility (LTCF) in Jerusalem. While previously identified host-related risk factors for colonization by these organisms undoubtedly contributed to these outbreaks, it is very likely that bacterial factors might be crucial in explaining the striking differences in transmissibility between the implicated strains. We therefore sought bacterial factors associated with these different epidemiological behaviours. METHODS: Seven CRKP isolated at our hospital and the LTCF during 2008-09 were examined by antimicrobial susceptibility testing and PFGE, and further analyses of these two clones was done using multilocus sequence typing and competition experiments. Plasmids were analysed by conjugation, restriction mapping, PCR and sequencing. RESULTS: Both clones were multidrug resistant and harboured identical plasmids carrying the bla(KPC-3) gene. The hyper-transmissible epidemic clone carried additional antibiotic resistance genes and hosted an additional plasmid. The clone from the LTCF did not demonstrate hyper-transmissible properties despite its presence in an institution of a type commonly plagued by the epidemic clone. Competition assays showed the more easily contained strain to be fitter. CONCLUSIONS: These findings suggest that neither the presence of the plasmid carrying the bla(KPC-3) gene nor relative survival fitness account for the hyper-transmissibility of the epidemic strain. The role of patient age in susceptibility to colonization by the epidemic strain should be investigated.

A carbapenem-resistant Klebsiella pneumoniae epidemic clone in Jerusalem: sequence type 512 carrying a plasmid encoding aac(6')-Ib.

OBJECTIVES: We characterized distinctive features of a hypertransmissible carbapenem-resistant Klebsiella pneumoniae (CRKP) clone that emerged at Hadassah Hospital, Ein-Kerem, Jerusalem, Israel, in 2006. METHODS: Eleven CRKP isolated at Hadassah Hospital during 2005-09 were examined by antimicrobial susceptibility testing, PFGE and multilocus sequence typing (MLST). Plasmids were analysed by conjugation, restriction mapping, PCR and sequencing. RESULTS: Divergence from the national epidemic sequence type (ST) ST258 to ST512 was observed early on. Carbapenem resistance was conferred by bla(KPC-3) carried on a plasmid apparently closely related to pKpQIL, also from Israel. This clone also carried a 15 kb plasmid, designated pAAC154, that carries a Tn1331 derivative containing the aac(6')-Ib gene. pAAC154 does not carry a bla(KPC) gene, but is similar to pS15, a plasmid from New York that carries bla(KPC-2). CONCLUSIONS: A single CRKP clone ST512 has spread efficiently in our region. In this clone, aac(6')-Ib, common in CRKP strains, is carried on a different plasmid from bla(KPC-3).

Bacteremia with Carbapenemase-Producing Enterobacterales in Immunocompromised Patients Colonized with These Bacteria.

We aimed to analyze rates and risk factors for carbapenemase-producing Enterobacterales (CPE) bloodstream infection (BSI) in CPE-colonized patients with malignancies or following hematopoietic cell transplantation. We retrospectively collected data on demography, underlying disease, colonizing CPE, treatment, intensive care unit (ICU) hospitalization, CPE-BSI, and mortality in CPE-colonized immunocompromised patients (2014-2020). Two hundred twenty-one patients were colonized with 272 CPE: 254 (93.4%) carried one carbapenemase [KPC (50.4%), NDM (34.6%), OXA-48-like (5.2%), and VIM (3.3%)]; 18 (6.6%) carried two carbapenemases. Twenty-eight (12.7%) patients developed CPE-BSI. Univariate analysis revealed CPE-BSI-associated factors: younger age, carbapenem or aminoglycoside exposure, ICU admission, neutropenia, carrying serine carbapenemase-producing, and specifically KPC-producing bacteria, colonization with several CPE, and detection of several carbapenemases. None of 23 auto-HSCT recipients developed CPE-BSI. In multivariate analysis, ICU hospitalization was significantly associated with CPE-BSI (odds ratio [OR] 2.82, 95% CI 1.10-7.20; p = 0.042); solid tumor diagnosis was protective (OR 0.21, 95% CI 0.05-1.01; p = 0.038). One-year crude mortality was 108/221 (48.8%), including 19/28 (67.9%) and 89/193 (46.1%) in patients with and without CPE-BSI, p = 0.104. To conclude, CPE-BSI is rare in CPE-colonized patients with solid tumors and following auto-HSCT. ICU hospitalization increased CPE-BSI risk. These data can help to guide empirical anti-CPE antibiotic therapy in patients colonized with these bacteria.

A Case Report of Mycoplasma hominis Subdural Empyema Following Decompressive Craniotomy, and a Review of Central Nervous System Mycoplasma hominis Infections.

Background: Mycoplasma hominis is a small cell-wall-free organism, part of the normal microbiota of the genitourinary tract. It is rarely involved in extragenital infections, mainly joint, surgical-site, and respiratory infections. Methods: We describe a case of M. hominis subdural empyema and lower limb surgical site infections, following decompressive craniotomy, after traumatic brain and extremities injury. In addition, a literature review of 34 cases M. hominis CNS infections was done. Results: Our case depicts a 25-years old patient who developed subdural empyema and surgical site infections in his cranium and fibula. Both sites were cultured, and small pinpoint colonies grew on blood agar. MALDI-TOF MS identified M. hominis. Simultaneously 16S-rDNA PCR from CSF detected M. hominis. Antimicrobial treatment was switched to doxycycline with improvement. Literature review revealed 21 adults and 13 pediatric cases of M. hominis CNS infection. Risk factors in adults were head trauma, neurosurgery, or post-partum period. Conclusions: Based upon the literature reviewed, we postulate that adult patients with head trauma or neurosurgical procedure, rarely are infected either through direct contamination during the trauma, or by undergoing urgent, urinary catheterization, and may experience distant infection due to translocation of M. hominis into the bloodstream. In such cases diagnosis is delayed due to difficulties in growing and identifying the bacteria. Empiric antimicrobials are usually not effective against mycoplasmas. These factors contributed to the mortality in adult cases (15%). Our rare case highlights the necessity of combining classical microbiology routines with advanced molecular techniques to establish a diagnosis in complicated cases.

Imipenem disc for detection of KPC carbapenemase-producing Enterobacteriaceae in clinical practice.

The global spread of class A-carbapenemase-producing Enterobacteriaceae has made the development of a simple test a desirable goal. A disc diffusion test using imipenem was 100% sensitive and 96% specific in identifying carbapenemase-producing organisms, potentially reducing or eliminating the need for the relatively labor-intensive modified Hodge test.

An outbreak of achromobacter xylosoxidans associated with ultrasound gel used during transrectal ultrasound guided prostate biopsy.

PURPOSE: We describe an outbreak of Achromobacter xylosoxidans after transrectal ultrasound guided prostate biopsy at a urology unit at a tertiary care center as well as clinical and microbiological investigation, and intervention. MATERIALS AND METHODS: In September 2008, several days after undergoing transrectal ultrasound guided prostate biopsy, 4 patients were hospitalized with fever. We reviewed the procedure and infection control practices in the urology service. Environmental cultures were obtained from equipment and materials used for the procedure. Isolates were identified by routine laboratory procedures with molecular confirmation and characterized by pulsed field gel electrophoresis. RESULTS: A. xylosoxidans was isolated from the urine of 2 patients, of whom 1 also had a positive blood culture. Review of transrectal ultrasound guided prostate biopsy revealed that the lubricant gel used in the procedure, which the biopsy needle passes through, was held in a plastic container that was repeatedly refilled from a large bag. A. xylosoxidans was isolated from this container. Pulsed field gel electrophoresis showed that the isolates obtained from patients and the gel were identical. CONCLUSIONS: Contaminated lubricant gel was the cause of this outbreak. The practice of repeatedly refilling gel containers with nonsterile gel was replaced by the use of individual sterile gel sachets in each patient. No further cases occurred. During an invasive procedure involving a sterile body site, such as transrectal ultrasound guided prostate biopsy, using sterile gel is essential. Our experience emphasizes the crucial need to review all invasive procedures from an infection control perspective.

The role of Staphylococcus lugdunensis as a pathogen in children: a multicentre retrospective study.

Introduction: Staphylococcus lugdunensis (SL), a tube coagulase negative Staphylococcus, is known to be pathogenic in adults, causing mainly skin infections.Gap Statement: Previous studies assessing SL's role in paediatric populations are sparse and are mainly limited to case reports.Aim: Present the clinical characteristics consistent with SL infections and its putative role as a pathogen in the paediatric population.Methodology: A retrospective multicentre study was conducted in four paediatric medical centres in Israel. Patients with isolates of SL presenting between 2009-2019 were included.Results: SL was isolated from 40 patients. Average (±SD) age at presentation was 5.9 (±6.2) years, with 22 (55 %) being female. Skin, soft tissue and musculoskeletal infections were the most common (n=20, 50%) followed by ear infections (n=13, 32.5%). Five cases of urine isolates and two isolates from blood culture samples were also reported. Skin abscess was the most common infection among skin and soft tissue isolates, reported in 17 children (85%) with SL being the only pathogen in 15 (75%). Otitis media was the most common ear infection accounting for 12 (92%) of all cases with SL as the only isolate reported in 6 (46%). Five cases of SL isolates from urine specimens were reported, all of which with poor growth of bacteria and normal urinalysis. Two cases of SL growth in blood culture were found in children presenting with signs and symptoms consistent with invasive blood stream infection.Conclusions: In the paediatric population, studied infections caused by SL are increasingly observed. The results of this study highlight its role as a pathogen in soft tissue infections and its putative role in otitis media and invasive blood stream infections. However, the role of SL as an uropathogen was not established.

Imported melioidosis, Israel, 2008.

In 2008, melioidosis was diagnosed in an agricultural worker from Thailand in the southern Jordan Valley in Israel. He had newly diagnosed diabetes mellitus, fever, multiple abscesses, and osteomyelitis. Burkholderia pseudomallei was isolated from urine and blood. Four of 10 laboratory staff members exposed to the organism received chemoprophylaxis, 3 of whom had adverse events.