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BACKGROUND Extended-spectrum β-lactamase (ESBL)-producing Enterobacterales-(Ent) infections are increasing in pediatrics. Before CTX-M ESBL emerged, the most common infection-associated ESBL genes were TEM and SHV-type ESBLs. We sought to define the current epidemiology of Ent infections in children due to blaTEM and blaSHV (TEM-SHV-Ent). METHODS A retrospective case-control analysis of children with TEM-SHV-Ent infections at 3 Chicago-area hospitals was performed. Cases had extended-spectrum-cephalosporin (ESC)-resistant infections due to blaTEM or blaSHV. DNA analysis assessed β-lactamase (bla) genes, multilocus sequence types, and E. coli phylogenetic grouping. Controls had ESC-susceptible Ent infections, matched 3:1 to cases by age, source, and hospital. Clinical-epidemiologic infection predictors were assessed. RESULTS Of 356 ESC-R-Ent isolates from children (median 4.3 years), 38 (10.7%) were positive solely for blaTEM-ESBL (26%) or blaSHV-ESBL genes (74%). Predominant organisms were Klebsiella (34.2%) and E. coli (31.6%); 67% of E. coli were phylogroup B2. Multilocus sequence types revealed multiple strains, 58% resistant to ≥3 antibiotic classes. On multivariable analysis, children with TEM-SHV-Ent infections more often had recent inpatient care (OR, 8.2), yet were diagnosed mostly as outpatients (OR, 25.6) and less in Neonatal Intensive Care Units (OR, 0.036) than controls. TEM-SHV-Ent patients had more gastrointestinal (OR, 23.7) and renal comorbidities (OR, 4.2). Differences in demographics, antibiotic exposure, and foreign bodies were not found. CONCLUSION TEM-SHV-Ent are commonly linked to inpatient exposures in children with chronic conditions but most often present in outpatient settings. Clinicians should be aware of the potential increased risk for TEM-SHV-Ent infections in outpatients with gastrointestinal and renal comorbidities and histories of prolonged hospital stays.

Background Fluoroquinolones are uncommonly prescribed in children, yet pediatric multidrug resistant (MDR) enterobacteriaceae (Ent) infections often reveal fluoroquinolone resistance (FQR). We sought to define the molecular epidemiology of FQR and MDR-Ent in children. Methods A case-control analysis of children with MDR-Ent infections at 3 Chicago hospitals was performed. Cases were children with third-generation cephalosporin-resistant and/or carbapenem-resistant Ent infections. Polymerase chain reaction and DNA analysis assessed bla and plasmid-mediated FQR (PMFQR) genes. Controls were children with third-generation cephalosporin, fluoroquinolone, and carbapenem-susceptible Ent infections matched by age, source and hospital. We assessed clinical-epidemiologic predictors of PMFQR Ent infection. Results Of 169 third-generation cephalosporin-resistant and/or carbapenem-resistant Ent isolates from children (median age, 4.8 years), 85 were FQR; 56 (66%) contained PMFQR genes. The predominant organism was Escherichia coli, and most common bla gene blaCTX-M-1 group. In FQR isolates, PMFQR gene mutations included aac6'1bcr, oqxA/B, qepA and qnrA/B/D/S in 83%, 15%, 13% and 11% of isolates, respectively. FQR E. coli was often associated with phylogroup B2, ST43/ST131. On multivariable analysis, PMFQR Ent infections occurred mostly in outpatients (odds ratio, 33.1) of non-black-white-Hispanic race (odds ratio, 6.5). Residents of Southwest Chicago were >5 times more likely to have PMFQR Ent infections than those in the reference region, while residence in Central Chicago was associated with a 97% decreased risk. Other demographic, comorbidity, invasive-device, antibiotic use or healthcare differences were not found. Conclusions The strong association of infection with MDR organisms showing FQR with patient residence rather than with traditional risk factors suggests that the community environment is a major contributor to spread of these pathogens in children.

The distribution of upper respiratory viral loads (VL) in asymptomatic children infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is unknown. We assessed PCR cycle threshold (Ct) values and estimated VL in infected asymptomatic children diagnosed in nine pediatric hospital testing programs. Records for asymptomatic and symptomatic patients with positive clinical SARS-CoV-2 tests were reviewed. Ct values were (i) adjusted by centering each value around the institutional median Ct value from symptomatic children tested with that assay and (ii) converted to estimated VL (numbers of copies per milliliter) using internal or manufacturer data., The distribution of upper respiratory viral loads (VL) in asymptomatic children infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is unknown. We assessed PCR cycle threshold (Ct) values and estimated VL in infected asymptomatic children diagnosed in nine pediatric hospital testing programs. Records for asymptomatic and symptomatic patients with positive clinical SARS-CoV-2 tests were reviewed. Ct values were (i) adjusted by centering each value around the institutional median Ct value from symptomatic children tested with that assay and (ii) converted to estimated VL (numbers of copies per milliliter) using internal or manufacturer data. Adjusted Ct values and estimated VL for asymptomatic versus symptomatic children (118 asymptomatic versus 197 symptomatic children aged 0 to 4 years, 79 asymptomatic versus 97 symptomatic children aged 5 to 9 years, 69 asymptomatic versus 75 symptomatic children aged 10 to 13 years, 73 asymptomatic versus 109 symptomatic children aged 14 to 17 years) were compared. The median adjusted Ct value for asymptomatic children was 10.3 cycles higher than for symptomatic children (P < 0.0001), and VL were 3 to 4 logs lower than for symptomatic children (P

Mycoplasma pneumoniae is a major cause of community-acquired pneumonia. There are limited data in the United States on the molecular epidemiological characteristics of M. pneumoniae We collected 446 M. pneumoniae-positive specimens from 9 states between August 2012 and October 2018. Culture, antimicrobial susceptibility testing, P1 subtyping, and multilocus VNTR (variable-number tandem repeats) analysis (MLVA) were performed to characterize the isolates. Macrolide-resistant M. pneumoniae (MRMp) was detected in 37 (8.3%) specimens. P1 subtype 2 (P1-2) was the predominant P1 subtype (59.8%). P1 subtype distribution did not change significantly chronologically or geographically. The macrolide resistance rate in P1 subtype 1 (P1-1) samples was significantly higher than that in P1-2 (12.9% versus 5.5%). Six P1-2 variants were identified, including two novel types, and variant 2c was predominant (64.6%). P1-2 variants were distributed significantly differently among geographic regions. Classical P1-2 was more frequent in lower respiratory tract specimens and had longer p1 trinucleotide repeats. Classical P1-2 was most common in MRMp (35.7%), while variant 2c was most common in macrolide-susceptible M. pneumoniae (67.5%). Fifteen MLVA types were identified; 3-5-6-2 (41.7%), 4-5-7-2 (35.3%), and 3-6-6-2 (16.6%) were the major types, and four MLVA clusters were delineated. The distribution of MLVA types varied significantly over time and geographic location. The predominant MLVA type switched from 4-5-7-2 to 3-5-6-2 in 2015. MLVA type was associated with P1 subtypes and P1-2 variant types but not with macrolide resistance. To investigate the M. pneumoniae genotype shift and its impact on clinical presentations, additional surveillance programs targeting more diverse populations and prolonged sampling times are required.

We evaluated six commercial molecular tests targeting Mycoplasma pneumoniae, namely, the BioFire FilmArray respiratory panel (RP), the Meridian Alethia Mycoplasma Direct, the GenMark ePlex respiratory pathogen panel (RPP), the Luminex NxTAG RPP, the ELITech ELITe InGenius Mycoplasma MGB research use only (RUO) PCR, and the SpeeDx Resistance Plus MP assays. Laboratory-developed PCR assays at the University of Alabama at Birmingham and the Centers for Disease Control and Prevention were used as reference standards. Among 428 specimens, 212 were designated confirmed positives for M. pneumoniae. The highest clinical sensitivities were found with the InGenius PCR (99.5%) and the FilmArray RP (98.1%). The Resistance Plus MP identified 93.3% of the confirmed-positive specimens, whereas 83.6, 64.6, and 55.7% were identified by the ePlex RPP, NxTAG RPP, and Mycoplasma Direct assays, respectively. There was no significant difference between the sensitivity of the reference methods and that of the FilmArray RP and InGenius assays, but the remaining four assays detected significantly fewer positive specimens (P

Antimicrobial stewardship can be challenging in children with bloodstream infections (BSIs) caused by Gram-negative bacilli (GNB). This retrospective cohort study explored how data elements in the electronic health record could potentially optimize empiric antibiotic therapy for BSIs caused by GNB, via the construction of customized antibiograms for categorical GNB infections and identification of opportunities to minimize organism-drug mismatch and decrease time to effective therapy. Our results suggest potential strategies that could be implemented at key decision points in prescribing at initiation, modification, and targeting of therapy.

There are sparse data to indicate the extent that macrolide-resistant Mycoplasma pneumoniae (MRMp) occurs in the United States or its clinical significance. Between 2015 and 2018, hospitals in 8 states collected and stored respiratory specimens that tested positive for M. pneumoniae and sent them to the University of Alabama at Birmingham, where real-time PCR was performed for detection of 23S rRNA mutations known to confer macrolide resistance. MRMp was detected in 27 of 360 specimens (7.5%). MRMp prevalence was significantly higher in the South and East (18.3%) than in the West (2.1%). A2063G was the predominant 23S rRNA mutation detected. MICs for macrolide-susceptible M. pneumoniae (MSMp) were ≤0.008 μg/ml, whereas MICs for MRMp were 16 to 32 μg/ml. Patients with MRMp infection were more likely to have a history of immunodeficiency or malignancy. Otherwise, there were no other significant differences in the clinical features between patients infected with MRMp and those infected with MSMp, nor were there any differences in radiographic findings, hospitalization rates, viral coinfections, the mean duration of antimicrobial treatment, or clinical outcomes. There was no significant change in MRMp incidence over time or according to age, sex, race/ethnicity, or status as an inpatient or an outpatient. Patients with MRMp were more likely to have received a macrolide prior to presentation, and their treatment was more likely to have been changed to a fluoroquinolone after presentation. This is the first national surveillance program for M. pneumoniae in the United States. Additional surveillance is needed to assess the clinical significance of MRMp and to monitor changes in MRMp prevalence.

Herpes simplex virus (HSV) is a common and often benign infection in humans; although it less commonly affects newborns, infection in this age group can be devastating. Newborns often present with nonspecific clinical findings, making timely and accurate diagnosis of infection critical. A wide variety of tests are available for detecting herpes simplex virus infection, but only a subset are useful and validated in the newborn population. The current review summarizes available diagnostic testing for neonatal disease, including discussing limitations, unmet needs, and emerging data on molecular testing methods.

BACKGROUND: Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacteriaceae (KPC-CRE) are multidrug-resistant organisms (MDRO) causing morbidity and mortality worldwide. KPC-CRE prevalence is increasing in pediatric populations, though multi-centered data are lacking. Identifying risk factors for KPC-CRE infection in children and classifying genotypes is a priority in this vulnerable population. METHODS: A case-case-control study of patients (0–22 years) at 3 tertiary-care Chicago-area medical centers, 2008–2015, was conducted. Case group 1 children possessed KPC-CRE infections; case group 2 harbored carbapenem-susceptible Enterobacteriaceae (CSE) infections; control had negative cultures. Case-control matching was 1:1:3 by age, infection site, and hospital. Statistical and molecular analyses were performed. RESULTS: Eighteen KPC-CRE infections were identified; median patient age was 16.5 years. Of 4 available KPC-CRE, two were unrelated, non-ST258 KP strains harboring bla(KPC-2), one was a ST258 KP harboring bla(KPC-3), and the last was an E. coli containing bla(KPC-2). KPC-CRE and CSE-infected patients had more MDRO infections, long-term care facility admissions, and lengths of stay (LOS) >7 days before culture. KPC-CRE and CSE patients had more gastrointestinal (GI) comorbidities (ORs 28.0 and 6.4) and ≥3 comorbidities (ORs 15.4 and 3.5) compared to controls; KPC-CRE patients had significantly more pulmonary and neurologic comorbidities (both ORs 4.4) or GI and pulmonary devices (ORs 11.4 and 6.1). Compared to controls, CSE patients had more prior fluoroquinolone use (OR 7.4); KPC-CRE patients had more carbapenem or aminoglycoside use (ORs 10.0 and 8.0). Race, gender, LOS, and mortality differences were insignificant. CONCLUSIONS: Pediatric patients with KPC-CRE infection suffer from high multi-system disease/device burdens and exposures to carbapenems and aminoglycosides. Different from adult reports, non-ST258 KP strains were more common, and LOS and mortality rates were similar in all groups. Pediatric CRE control in should focus on modifiable risk factors including antibiotic and device utilization.

Implementing matrix-assisted laser desorption ionization-time of flight and multiplex polymerase chain reaction has been associated with decreased mortality and hospital length of stay in adults, but the impact in pediatrics is less understood.This pre-post quasi-experimental study compared antibiotic prescribing for positive blood cultures in patients ≤21 years of age collected in 2012 (preintervention) and in 2015 (after matrix-assisted laser desorption ionization-time of flight/multiplex polymerase chain reaction). Time to effective and optimal antimicrobial therapy was evaluated using Cox proportional hazards regression. Time to ideal optimal therapy was estimated as the earliest potential initiation of optimal therapy. Antibiotic use and clinical outcomes were measured.There were 242 and 192 positive monomicrobial blood cultures in 2012 and 2015, respectively. Postintervention, time to optimal therapy (73.8 vs. 48.8 hours; P0.001) and organism identification (55.6 vs. 29.5 hours; P0.001) were reduced, and patients were more likely to receive optimal therapy by 7 days (hazard ratio, 1.85; P0.001). In the ideal scenario in 2015, there was an 8.8-hour delay in initiating optimal therapy based on the time that sufficient microbiologic data were available. Postintervention, time to effective therapy (2.8 vs. 2.7 hours; P = 0.782) and clinical outcomes did not differ. Unnecessary antibiotic duration for probable contaminants (skin flora) (43.1 vs. 29.7 hours; P = 0.027), vancomycin for methicillin-sensitive Staphylococcus aureus (54.0 vs. 41.3 hours; P = 0.008) and nonpenicillin/ampicillin antibiotics for group A Streptococcus, group B Streptococcus and Enterococcus faecalis (87.2 vs. 33.4 hours; P0.001) were reduced postintervention.Rapid diagnostics reduced time to optimal antimicrobial therapy and unnecessary antibiotic use without worse clinical outcomes.

Group A streptococcal (GAS) pharyngitis is a particularly important condition in areas of New Zealand where the incidence of acute rheumatic fever remains unacceptably high. Prompt diagnosis and treatment of GAS pharyngitis are cornerstones of the Rheumatic Fever Prevention Programme, but these are hindered by the turnaround time of culture. Tests with excellent performance and rapid turnaround times are needed. For this study, throat swabs (Copan ESwabs) were collected from schoolchildren self-identifying with a sore throat. Samples were tested by routine culture and the illumigene GAS assay using loop-mediated isothermal amplification. Discrepant results were resolved by retesting of the same specimen by an alternative molecular assay. Seven hundred fifty-seven throat swab specimens were tested by both methods. The performance characteristics of the illumigene assay using culture on blood agar as the “gold standard” and following discrepancy analysis were as follows: sensitivity, 82% and 87%, respectively; specificity, 93% and 98%, respectively; positive predictive value, 61% and 88%, respectively; and negative predictive value, 97% and 97%, respectively. In our unique setting of a school-based throat swabbing program, the illumigene assay did not perform quite as well as described in previous reports. Despite this, its improved sensitivity and rapid turnaround time compared with those of culture are appealing.

Transitioning from administration of monthly palivizumab to a single dose at discharge was associated with substantial pharmacy cost savings. With the concurrent adoption of private hospital rooms and visitor restriction policies, hospital-wide and neonatal intensive care unit healthcare-associated respiratory syncytial virus infections decreased following these changes.Infect Control Hosp Epidemiol 2018;39:485–487

Macrolide-resistant Mycoplasma pneumoniae (MRMP) is highly prevalent in Asia and is now being reported from Europe. Few data on MRMP are available in the United States. Using genotypic and phenotypic methods, we detected high-level MRMP in 13.2% of 91 M. pneumoniae­–positive specimens from 6 US locations.

An international multilaboratory collaborative study was conducted to develop standard media and consensus methods for the performance and quality control of antimicrobial susceptibility testing of Mycoplasma pneumoniae , Mycoplasma hominis , and Ureaplasma urealyticum using broth microdilution and agar dilution techniques. A reference strain from the American Type Culture Collection was designated for each species, which was to be used for quality control purposes. Repeat testing of replicate samples of each reference strain by participating laboratories utilizing both methods and different lots of media enabled a 3- to 4-dilution MIC range to be established for drugs in several different classes, including tetracyclines, macrolides, ketolides, lincosamides, and fluoroquinolones. This represents the first multilaboratory collaboration to standardize susceptibility testing methods and to designate quality control parameters to ensure accurate and reliable assay results for mycoplasmas and ureaplasmas that infect humans.

Rapid diagnosis of staphylococcal bacteremia directs appropriate antimicrobial therapy, leading to improved patient outcome. We describe herein a rapid test (Staphylococcus to the species level as well as the presence or absence of the methicillin resistance determinant gene, mecA . The test, Staph ID/R, combines a rapid isothermal nucleic acid amplification method, helicase-dependent amplification (HDA), with a chip-based array that produces unambiguous visible results. The analytic sensitivity was 1 CFU per reaction for the mecA gene and was 1 to 250 CFU per reaction depending on the staphylococcal species present in the positive blood culture. Staph ID/R has excellent specificity as well, with no cross-reactivity observed. We validated the performance of Staph ID/R by testing 104 frozen clinical positive blood cultures and comparing the results with rpoB gene or 16S rRNA gene sequencing for species identity determinations and mecA gene PCR to confirm mecA gene results. Staph ID/R agreed with mecA gene PCR for all samples and agreed with rpoB /16S rRNA gene sequencing in all cases except for one sample that contained a mixture of two staphylococcal species, one of which Staph ID/R correctly identified, for an overall agreement of 99.0% ( P < 0.01). Staph ID/R could potentially be used to positively affect patient management for Staphylococcus -mediated bacteremia.

A total of 116 clinical isolates collected in 2003 from a tertiary pediatric hospital and a primary pediatric department in Chicago, IL, were screened for reduced susceptibility to selected fluoroquinolones by disc diffusion. Correlation between reduced susceptibility and point mutations in the quinolone resistance-determining region of parC and gyrA genes was evaluated, and point mutations were compared with other reports of isolates derived from adult or mixed patient populations. Nine percent of isolates had reduced susceptibility to 1 or more of these fluoroquinolones by Etest: ciprofloxacin, levofloxacin, and moxifloxacin. A single point mutation (Ser-79) in parC seemed responsible for the reduced susceptibility. Resistant Streptococcus pyogenes isolates were compared using M/emm type, repetitive sequence-based PCR (rep-PCR), and pulsed-field gel electrophoresis (PFGE). Rep-PCR provided no more separation of strains than M/emm typing, and PFGE results with SgrAI were more discriminatory than with SmaI. The majority of these isolates were M/emm type 6. PFGE analysis using SgrAI demonstrated 2 different resistant strains among the M/emm type 6 isolates. The findings suggest that a population of S. pyogenes with an intrinsic reduced susceptibility to fluoroquinolones exists in pediatric clinical isolates. Monitoring of amino acid changes in both parC and gyrA will assist in the prediction of emergence of high-level fluoroquinolone resistance.

Two separate species of Ureaplasma have been identified that infect humans: Ureaplasma parvum and Ureaplasma urealyticum. Most notably, these bacteria lack a cell wall and are the leading infectious organism associated with infection-related induction of preterm birth. Fourteen separate representative prototype bacterial strains, called serovars, are largely differentiated by the sequence of repeating units in the C-terminus of the major surface protein: multiple-banded antigen (MBA). Monoclonal antibodies that recognise single or small groups of serovars have been previously reported, but these reagents remain sequestered in individual research laboratories. Here we characterise a panel of commercially available monoclonal antibodies raised against the MBA and describe the first monoclonal antibody that cross-reacts by immunoblot with all serovars of U. parvum and U. urealyticum species. We also describe a recombinant MBA expressed by Escherichia coli which facilitated further characterisation by immunoblot and demonstrate immunohistochemistry of paraffin-embedded antigens. Immunoblot reactivity was validated against well characterised previously published monoclonal antibodies and individual commercial antibodies were found to recognise all U. parvum strains, only serovars 3 and 14 or only serovars 1 and 6, or all strains belonging to U. parvum and U. urealyticum. MBA mass was highly variable between strains, consistent with variation in the number of C-terminal repeats between strains. Antibody characterisation will enable future investigations to correlate severity of pathogenicity to MBA isoform number or mass, in addition to development of antibody-based diagnostics that will detect infection by all Ureaplasma species or alternately be able to differentiate between U. parvum, U. urealyticum or mixed infections.

Most children with Clostridium difficile infection (CDI) experience community onset of CDI symptoms.We retrospectively compared hospital-onset healthcare facility-associated CDI cases to community-associated (CA) CDI cases diagnosed by Cepheid Xpert tcdB polymerase chain reaction (PCR) at an academic children's hospital over a 1-year period. Saved stools from CDI cases additionally underwent anaerobic stool culture and multiplex gastrointestinal pathogen PCR testing.Compared with 25 hospital-onset healthcare facility-associated CDI cases, the 74 CA-CDI cases were more frequently2 years old (18% vs. 0%, P = 0.034) and less frequently had antibiotic exposure in the past 30 days (26% vs. 88%, P0.0001), proton pump inhibitor exposure (16% vs. 36%, P = 0.036) or a gastrostomy tube (11% vs. 32%, P = 0.013). Among children diagnosed with CA-CDI, 19 (26%) had no identified CDI risk factors (immunocompromised; gastrostomy tube; recent antibiotic, proton pump inhibitor or inpatient/outpatient healthcare exposures). Clinical testing for viral pathogens was uncommon among children thought to have CA-CDI. Multiplex PCR testing of saved stool samples failed to identify C. difficile among 23% of cases diagnosed with CA-CDI by the Cepheid Xpert tcdB PCR assay. CDI antibiotic therapy was provided to nearly all patients testing positive by tcdB PCR irrespective of CDI risk factors.Many children diagnosed with CA-CDI by PCR lack CDI risk factors and have discordant results when additional CDI testing methods are performed, suggesting overdiagnosis of CDI in children with community-onset diarrhea. More selective CDI testing of low-risk pediatric patients is needed to more accurately diagnose CDI and limit unnecessary CDI antibiotic treatment in children.

Mycoplasma pneumoniae -positive clinical specimens obtained from the United States and China during the same period were studied for their molecular characteristics. We found much more diverse genotypes and a lower prevalence of macrolide resistance in the U.S. specimens. Data from the study also showed an association of the resistance with certain genotypes.

Three commercial molecular assays for detecting Mycoplasma pneumoniae were evaluated for their relative performances and hands-on time. They performed comparably well in clinical sensitivity and specificity.

Abiotrophia and Granulicatella species have been associated with various infections. Antimicrobial susceptibility data for these nutritionally variant streptococcus-like organisms, especially for pediatric isolates, are very limited. Little is known about the genetic bases of their resistance mechanisms. We report the results of identification to bacterial species level, antimicrobial susceptibility testing, macrolide resistance testing, and detection of genes encoding that resistance for a collection of 15 pediatric clinical isolates from normally sterile sites. Our results indicate that the prevalence of beta-lactam and macrolide resistance is high and that both erm and mef are found in these isolates.

We characterized 32 levofloxacin-nonsusceptible Streptococcus pneumoniae (LNSP) isolates obtained from a broad geographic region of North America over a 5-year period by using capsular serotypes, antimicrobial susceptibility profiles, BOX-PCR, multilocus sequence typing (MLST), and pulsed-field gel electrophoresis (PFGE). Sixteen international clones identified by the Pneumococcal Molecular Epidemiology Network also were included for comparison. Fifteen serotypes were represented, with serogroups 6, 9, 14, 19, and 23 accounting for 63% of isolates. Among isolates whose quinolone resistance-determining regions were sequenced, all contained gyrA and parC point mutations. Sixty-three percent were penicillin susceptible, and 84% were erythromycin susceptible. BOX-PCR analysis identified 39 different band patterns among 32 LNSP and 16 international clones and grouped 16 isolates, including 2 international clones, into seven unrelated groups of 2 to 4 isolates each. PFGE analysis identified 35 different band patterns among 32 LNSP and 16 international clones and grouped 21 isolates, including 3 international clones, into eight unrelated groups of 2 to 6 isolates each. MLST performed on 10 isolates identified five allelic profiles and separated 9 isolates into four groups of 2 to 3 isolates each. Overall, each typing method indicated that the LNSP were heterogeneous and that resistance to fluoroquinolones was not closely associated with a particular serotype or with coresistance to other antimicrobial classes and suggests that LNSP have likely arisen through independent mutational events as a result of selective pressure. However, seven LNSP were found to be related to three international clones by PFGE.

The performance of the FilmArray blood culture identification (BCID) panel has been studied in adult patients. We describe here an evaluation of this assay for the rapid identification of pathogens in Bactec Peds Plus/F and Bactec standard anaerobic/F bottles that contained blood samples from pediatric patients at a tertiary care children's hospital.

We describe the clinical course of four patients who had Trichosporon mycotoxinivorans recovered from multiple sputum cultures over time with various clinical consequences but no fatalities. We also report successful rapid identification of this organism using matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry.

We retrospectively studied 306 pediatric methicillin-resistant Staphylococcus aureus isolates collected in 2000/2001, 2003, 2005, and 2007 for possible vancomycin minimum inhibitory concentration (MIC) change over time using Etest, agar dilution, and broth microdilution (MicroScan) methods. Vancomycin MICs did not increase. Inducible clindamycin resistance declined significantly (53%-0%, P < 0.001). Considerably different proportions of isolates with vancomycin MIC = 2 microg/mL were identified by different laboratory methodologies, suggesting the need for caution in their interpretation and in comparing published data. During this period the proportion of USA300 strains increased dramatically.

Inflammatory pseudotumor (IPT) of the heart is rare and of unknown etiology. We present a case of cardiac IPT caused by Listeria monocytogenes that evolved following gastroenteritis in a previously healthy child. L. monocytogenes, known to cause acute invasive infections, has not been reported previously as a cause of cardiac infection in children or of IPT. The literature concerning infectious IPT is reviewed.

We describe the first pediatric case of Gemella bergeriae endocarditis in a 15-year-old boy with tetralogy of Fallot and pulmonary atresia who presented with weight loss, chills, and cold intolerance. Blood cultures revealed Gram-positive cocci that failed to type with Lancefield group antiserum. The identification of the organism was confirmed by 16S rRNA gene sequencing.

E-test, Vitek 2, MicroScan, agar dilution, and disk diffusion were compared for detection of decreased linezolid susceptibility due to 23S rRNA gene G2576T mutation among 32 clinical Enterococcus strains initially reported as intermediate or resistant by E-test alone or Vitek 2 confirmed by E-test. Agar and broth dilution methods were in concordance with PCR detection of the mutation, and disk diffusion was somewhat less sensitive but equally specific.

The performance of the Illumigene group A Streptococcus assay was evaluated by comparing it to culture using 437 consecutive throat swabs. The Illumigene assay was also directly compared to PCR with 161 samples. This Illumigene assay is rapid and easy to perform. The assay also has high sensitivity (100%) compared to culture or PCR and high specificity (99.2%) compared to PCR. A total of 8.8% of the isolates were erythromycin resistant, and 6.9% were clindamycin resistant.

One of the major surface structures of Ureaplasma urealyticum recognized by antibodies of patients during infection is the MB antigen. Previously, we showed by Western blot (immunoblot) analysis that any one of the anti-MB monoclonal antibodies (MAbs) 3B1.5, 5B1.1, and 10C6.6 could block the binding of patient antibodies to MB. Subsequent DNA sequencing revealed that a unique six-amino-acid direct tandem repeat region composed the carboxy two-thirds of this antigen. In the present study, using antibody-reactive peptide scanning of this repeat region, we demonstrated that the amino acids defining the epitopes for MAbs 3B1.5 5B1.1 and 10C6.6 are EQP, GK, and KEQPA, respectively. Peptide scanning analysis of an infected patient's serum antibody response showed that the dominant epitope was defined by the sequence PAGK. Mapping of these continuous epitopes revealed overlap between all MAb and patient polyclonal antibody binding sites, thus explaining the ability of a single MAb to apparently block all polyclonal antibody binding sites. We also show that a single amino acid difference in the sequence of the repeats of serovars 3 and 14 accounts for the lack of reactivity with serovar 14 of two of the serovar 3-specific MAbs. Finally, the data demonstrate the need to obtain the sequences of the mba genes of all serovars before an effective serovar-specific antibody detection method can be developed.

Pasteurella multocida has been reported to cause peritoneal dialysis-associated peritonitis after a cat bite or scratch to the catheter. We report a teenager with hamster bite peritonitis caused by P. aerogenes, an organism predominantly isolated from swine.

It is becoming apparent that a high rate of variability of surface structures is a ubiquitous property among mycoplasmas. The present study demonstrates how variations in the size of the V-1 antigen (a major surface antigen of Mycoplasma pulmonis thought to be associated with virulence) are reflected by phenotypic differences (cytadherence) that may play a role in virulence of the organism. Furthermore, a similar antigen is described for the human pathogen Urea-plasma urealyticum, and data are presented on the analysis of clinical isolates that demonstrate the potential for variation in the size of this antigen in vivo. Although no direct connection of antigen variation to natural disease has yet been presented, the data further document the tremendous potential for virulence-related diversity possessed by these organisms and emphasize the importance of a valid animal model for discerning the true relationship between variation and virulence.

The 2009 H1N1 influenza virus has rapidly spread all over the world. At this time, regions in the northern hemisphere are at the beginning of the typical annual respiratory virus season, although the 2009 H1N1 virus has been highly prevalent for the last several months. This year, it is likely that

In the summer and fall of 2007, we observed a unique cluster of cases of severe coxsackievirus B1 (CVB1) infection among Chicago area neonates. Eight neonates had closely related strains of CVB1 that were typed at the Centers of Disease Control and Prevention; 2 other neonates had CVB infections, 1 of which was further identified as serotype CVB1. All had severe myocarditis; 1 neonate underwent heart transplantation, and 1 died of severe left ventricular dysfunction.

Background Enterovirus infections are very common and typically cause mild illness, although neonates are at higher risk for severe illness. In 2007, the Centers for Disease Control and Prevention (CDC) received multiple reports of severe neonatal illness and death associated with coxsackievirus B1 (CVB1), a less common enterovirus serotype not previously associated with death in surveillance reports to the CDC. Methods This report includes clinical, epidemiologic, and virologic data from cases of severe neonatal illness associated with CVB1 reported during the period from 2007 through 2008 to the National Enterovirus Surveillance System (NESS), a voluntary, passive surveillance system. Also included are data on additional cases reported to the CDC outside of the NESS. Virus isolates or original specimens obtained from patients from 25 states were referred to the CDC picornavirus laboratory for molecular typing or characterization. Results During 2007-2008, the NESS received 1079 reports of enterovirus infection. CVB1 accounted for 176 (23%) of 775 reported cases with known serotype, making it the most commonly reported serotype for the first time ever in the NESS. Six neonatal deaths due to CVB1 infection were also reported to the CDC during that time. Phylogenetic analysis of the 2007 and 2008 CVB1 strains indicated that the increase in cases resulted from widespread circulation of a single genetic lineage that had been present in the United States since at least 2001. Conclusions Healthcare providers and public health departments should be vigilant to the possibility of continuing CVB1-associated neonatal illness, and testing and continued reporting of enterovirus infections should be encouraged.

Respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) are two important viral pathogens that cause respiratory tract infections in the pediatric population. The rapid detection of these agents allows the prompt isolation and treatment of infected patients. In the present prospective study, we evaluated the performances of four rapid antigen detection assays, including a rapid chromatographic immunoassay (CIA) for RSV (Directigen EZ RSV; Becton Dickinson, Sparks, MD), a direct fluorescent-antibody assay (DFA) for RSV (Bartels; Trinity Biotech, Carlsbad, CA), and two DFAs for hMPV manufactured by Diagnostic Hybrids Inc. (DHI; Athens, OH) and Imagen (Oxoid Ltd., Basingstoke, Hampshire, United Kingdom). The clinical specimens tested comprised 515 nasopharyngeal aspirates submitted to the Clinical Microbiology Laboratory at Hartford Hospital from 1 November 2006 to 21 April 2007. Compared to the results of real-time reverse transcription-PCR (RT-PCR), the CIA had a sensitivity of 79.8% and a specificity of 89.5%. The RSV DFA with Bartels reagents showed a sensitivity of 94.1% and a specificity of 96.8%. For hMPV, the sensitivity and specificity were 62.5% and 99.8%, respectively, for the DHI DFA and 63.2% and 100%, respectively, for the Imagen DFA. The hands-on and test turnaround times for CIA were 10 and 30 to 60 min, respectively, and the hands-on and test turnaround times for the RSV and hMPV DFAs were 30 and 105 min, respectively. We conclude that while the RSV CIA is user-friendly, it lacks sensitivity and specificity, especially during off-peak months. In contrast, the RSV DFA is more sensitive and specific, but interpretation of its results is subjective and it demands technical time and expertise. Similarly, both hMPV DFAs are highly specific in comparison to the results of RT-PCR, but their sensitivities await further improvements.

Adenovirus infection is an important cause of morbidity and mortality in stem cell transplant recipients. We report species and type-specific analysis from a prospective study of high-risk adenovirus infections following hematopoietic progenitor cell transplantation prior to, during, and after treatment with cidofovir, as well as species analysis of contemporaneously collected samples from control patients. Nine different adenovirus types representing all six recognized species were identified, and mixed infections were commonly found in this group of patients.

Fungal infections caused by Fusarium in the immunocompromised host are highly resistant to all antifungal agents. Fusarium endocarditis is a rare and usually fatal disease. We report an immunocompromised child who survived Fusarium solani endocarditis despite the in vitro resistance of the organism to all available antifungal agents.

Rapid detection of the Mycobacterium tuberculosis complex is important in patient management in terms of initiating appropriate antimycobacterial therapy as well as controlling the spread of this pathogen. Although mycobacterial culture continues to be a valuable diagnostic tool, the results are not rapid. The Centers for Disease Control and Prevention as well as the American Thoracic Society recommends obtaining mycobacterial cultures of at least three sputum specimens from patients in whom tuberculosis is suspected. In contrast to the increased time required for mycobacterial culture, acid-fast bacillus (AFB) staining generally provides rapid evidence for the presence of mycobacteria in a clinical specimen. AFB staining is used by most health care facilities to determine when patients with suspected tuberculosis should be isolated. However, AFB smears will be positive in only 60% of tuberculosis cases (7). Moreover, a recent study found that only 8.6% of patients placed in isolation proved to have tuberculosis yet 19% of patients with pulmonary tuberculosis were not isolated on the first day after hospital admission (9). Although AFB staining and mycobacterial culture are still the primary diagnostic tests in most laboratories, molecular tests based on nucleic acid amplification techniques have been available for the detection of the M. tuberculosis complex in a variety of clinical specimens (2, 4, 6). We used a colorimetric microtiter plate PCR-enzyme immunoassay (PCR-EIA) (8) targeting two specific genes for the rapid detection of the M. tuberculosis complex. One primer set (IS-1, 5′-CCT GCG AGC GTA GGC GTC GG-3′, and IS-2, 5′-CTC GTC CAG CGC CGC TTC GG-3′) was designed to target IS6110, an insertion sequence within the chromosome of M. tuberculosis (2). Another primer set (MPB-1, 5′-GAG GAG TTG AAA GGC ACC GAT-3′, and MPB-2, 5′-CGC GTC TGG GCG ATG TA-3′) was designed to target an M. tuberculosis gene which encodes the MPB64 protein (6). Two M. tuberculosis complex-specific 5′-biotinylated capture probes (IS-p, 5′-GGC GAA CCC TGC CCA GGT CGA CAC-3′, and MPB-p, 5′-CGG CCA GGC GTG CCA GAT TC-3′) were incorporated into a colorimetric signal amplification procedure to detect and confirm the amplification products as previously described (8). A similar format was used separately to amplify the human β-actin gene to assure the quality of extracted DNA samples. During a study period from December 2001 until January 2002, a total of 782 respiratory specimens, mainly sputa, were sent to the Diagnostic Laboratory Services, Inc., in Honolulu, Hawaii, for AFB staining and mycobacterial culture. Standard sample decontamination with N-acetyl-l-cysteine-NaOH (2% final concentration) and concentration by centrifugation were performed as described previously (5, 10). The volume of the final sediment was approximately 2 ml. Part of the sediment was used for the AFB smear, which was then stained using auramine-rhodamine fluorochrome staining (10). Part of the sediment was inoculated onto Middlebrook 7H10 solid medium and into BACTEC 12B broth bottles that were monitored for growth using the BACTEC 460TB instrument (Becton Dickinson, Sparks, Md.). Of these specimens, all 15 M. tuberculosis culture-positive specimens and 60 M. tuberculosis culture-negative specimens (which represented 7.8% of all collected M. tuberculosis-negative specimens) were included in the study. Of 75 specimens, 26 (34.7%) grew one or more types of mycobacteria. Of the positive mycobacterial cultures, 15 had the M. tuberculosis complex, 5 had the M. avium complex, 2 had M. simiae, 2 had M. chelonae, 1 had M. fortuitum, and 1 had the M. avium complex and M. chelonae. Nine of 15 specimens which grew the M. tuberculosis complex upon culture were positive by AFB staining, giving a sensitivity of 60%. A specimen that grew the M. avium complex upon culture was also positive by AFB staining, giving a specificity of 98%. The remaining specimens, having grown non-M. tuberculosis complex mycobacterial species, were negative by AFB staining. Nucleic acid was then extracted directly from 0.2 ml of N-acetyl-l-cysteine-NaOH-decontaminated and concentrated sediments by using IsoQuick (Orca Research, Inc., Bothell, Wash.) according to the manufacturer's instructions, as previously described (8). Extracted DNA was resuspended in 25 μl of water, and 10 μl of extracts was included in a PCR master mixture for PCR amplification (8). A housekeeping gene, human β-actin, was detectable in all DNA samples, indicating that these DNA samples were free of amplification inhibitors. All extracted DNA samples were tested for the M. tuberculosis complex by PCR-EIA targeting both IS6110 and MPB64 genes. M. tuberculosis complex-specific DNA was detected in 13 of 15 specimens that were culture positive for the M. tuberculosis complex, giving a sensitivity of 87%. Only two culture-positive specimens were PCR-EIA negative; both were also negative by AFB staining. All 60 respiratory specimens that were negative by culture were also negative by PCR-EIA, giving a specificity of 100%. These data indicated that PCR-EIA provides more rapid detection of the M. tuberculosis complex in clinical specimens than does AFB staining, with sensitivity improving from 60 to 87% and specificity improving from 98 to 100%. While our study population in Hawaii still has a relatively high incidence of tuberculosis, other hospitals now face a change in tuberculosis epidemiology. Tuberculosis has become a relatively uncommon disease in the continental United States in recent years. As a result, physicians have less experience with the disease and may have difficulty recognizing it, a circumstance potentially leading to misdiagnosis and spread of the infection (3). As the incidence of tuberculosis declines, more resources will be used inappropriately for patients whose culture specimens grow mycobacteria other than M. tuberculosis. A recent study prospectively assessed the management of patients with suspected tuberculosis in an area with a high prevalence of mycobacteria other than M. tuberculosis and a low incidence of tuberculosis. The high prevalence of mycobacteria other than M. tuberculosis in specimens has a substantial impact on the management of suspected tuberculosis. Clinicians' assessments were sensitive for tuberculosis but had poor predictive value. Owing to a high rate of isolation of mycobacteria other than M. tuberculosis, AFB staining was a weak predictor of tuberculosis, with a positive predictive value of only 33% (1). Therefore, development of additional techniques to enhance the early diagnostic predictive values given by AFB staining will be of benefit in addressing this problem. Although several nucleic acid amplification-based M. tuberculosis complex detection kits are commercially available, they are relatively expensive and the procedure is time-consuming (4). PCR-EIA as described in this report is simple, rapid, and user friendly. The whole procedure, including specimen processing, DNA extraction, PCR amplification, and amplicon identification, can be completed within an 8-h shift. An additional signal amplification step included in the microtiter plate system enhances test sensitivity, making this test an alternative to the AFB smear test in the clinical setting for tuberculosis patient management.

A total of 120 pleural fluid specimens from 113 pediatric patients were tested using two rapid antigen detection assays for Streptococcus pyogenes . Results were compared to culture, Gram stain, and PCR results. Each rapid antigen assay detected 9 out of 10 (90%) PCR-positive samples, with 100% specificity. These antigen detection assays are useful to provide microbiological diagnosis of empyema caused by S. pyogenes .

Thirty Streptococcus pneumoniae clinical isolates resistant to levofloxacin were analyzed for the quinolone resistance-determining DNA sequences to identify point mutations and were tested for in vitro susceptibility to multiple drug classes. Of these isolates, 29 had mutations in both gyrA and parC genes of DNA gyrase and topoisomerase IV, respectively. In GyrA, an amino acid change from Ser-81Phe was detected in 27 isolates and a Glu-85 Lys change was found in the remaining three. Of the 29 isolates for which ParC data were available, Ser-79 Tyr or Phe were the predominant mutations observed. MICs for levofloxacin were 4–16 mg/l, whereas those for moxifloxacin were 1–2 mg/l. Twenty-four (80%) isolates were susceptible to erythromycin, 25 (83%) to azithromycin, 26 (87%) to clarithromycin, 27 (90%) to clindamycin, 20 (67%) to penicillin, 21 (70%) to ceftriaxone and 30 (100%) to amoxycillin/clavulanate. These results confirm the presence of double mutations among clinical isolates of S. pneumoniae from diverse geographical regions of North America and also suggest that quinolone resistance may develop independently of resistance to other drug classes. © 2001 Elsevier Science B.V. and International Society of Chemotherapy. All rights reserved.

Contamination of broth cultures of acid-fast bacilli (AFB) by bacterial species other than Mycobacterium species frequently occurs. Many of these contaminated cultures require redecontamination and reincubation before the appropriate tests can be performed for identification, significantly affecting the turnaround time for reporting culture results. In this study, the Amplified Mycobacterium Tuberculosis Direct Test (MTD; Gen-Probe) was performed to detect the Mycobacterium tuberculosis complex (MTBC) in 125 BACTEC 12B broth cultures with positive growth indices. Among these, 41 grew non-AFB bacteria only, and all 41 were negative by the MTD. The remaining 84 bottles contained contaminated cultures that grew both AFB and other bacteria or yeasts. Repeat decontamination and reincubation of these specimens required a mean time of 13 days (range, 3 to 40 days). The MTD results were positive for 10 samples, 9 of which were MTBC culture positive and 1 of which grew Myobacterium celatum , a species known to cross-react in the MTD. All cultures growing other mycobacterial species were negative by the MTD. The results of this study demonstrate that the MTD is both sensitive and specific in detecting MTBC in contaminated broth cultures and that, when used selectively, the MTD can potentially rule in or out a diagnosis of MTBC as much as 12 days earlier than using nonamplified DNA probe testing alone can.

A branched-DNA (bDNA) signal amplification method was used to detect the mecA gene directly from blood culture broth growing staphylococci. BACTEC blood culture bottles with positive growth indices and containing staphylococcus-like organisms as shown by Gram stain were tested for the presence of the mecA gene. Comparison of test results was done among 225 patients (one blood culture from each patient). Compared with PCR, the sensitivity and specificity of the bDNA method are 100 and 99%, respectively. The bDNA test is carried out in a 96-well format and requires approximately 6 h to perform. Our preliminary results suggest that direct detection of the mecA gene by bDNA signal amplification is (i) sensitive enough to detect mecA directly from blood culture bottles without the requirement for subculture and (ii) as sensitive and specific as the PCR-based method.

Methicillin resistance in clinical isolates of Staphylococcus is thought to occur as a combined result of the expression of the mecA gene, which codes for the cell wall surrogate enzyme penicillin binding protein (PBP) 2a or 2′ and several factors such as the fem gene series or auxiliary (aux) genes (reviewed in reference 5). In clinical laboratories, antibiotic resistance is usually detected by using methods that require a viable culture of the organism and phenotypic expression of resistance genes. However, studies indicate that there is heterogeneous expression of PBP 2a that is dependent on environmental conditions (1, 10, 16). In addition, some isolates have been shown to exhibit low- or moderate-level methicillin resistance due to overproduction of β-lactamase, modifications in the PBP binding affinities, or the presence of expression factors not related to the mecA gene (2, 9, 12, 20). Variations in laboratory reporting of high-level methicillin resistance, which requires treatment with vancomycin, may be responsible for unnecessary vancomycin usage. The current guidelines from the Centers for Disease Control and Prevention suggest restriction of vancomycin use in order to slow the occurrence of vancomycin resistance in staphylococci (4). Molecular diagnostic assays, which detect genetic targets irrespective of expression level, have proven useful for the identification of isolates containing mecA. In recent years, several genotypic detection methods have been described (3, 7, 11, 14, 17). Most are PCR based, and some are multiplexed with broad-range 16S ribosomal DNA primers to assess the lysis efficiency of each assay. While these assays are highly sensitive and specific, we have found that they are time-consuming and PCR failures may occasionally occur due to lysis inefficiency or inhibitory substances. In the past, assays utilizing branched-DNA (bDNA) technology have been developed to detect antibiotic resistance markers as well as pathogenic agents in clinical samples (6, 19). This assay uses multiple probes that cause an amplification of chemiluminescent signal rather than the amplification of a genetic target that is observed in PCR-based assays. To avoid the complications observed with other tests, we developed a mecA-specific assay that uses bDNA technology to detect the gene in lysates derived from bacterial colonies isolated on solid media and directly from blood cultures. The assay is performed in a 96-well microtiter plate format and takes approximately 6 h to complete, thereby allowing same-day results for cultures containing staphylococci. (Portions of this work were presented at the Conference on Molecular Diagnostics and Therapeutics, Kananaskis, Alberta, Canada, 15–19 August 1997, and the 37th Interscience Conference on Antimicrobial Agents and Chemotherapy, Toronto, Ontario, Canada, 28 September–1 October 1997.)

Mycoplasma hominis is a commensal in the genital tract of women and has been associated with urogenital and extragenital infections. However, central nervous system infections with this organism in adults are very rare. Here we describe the recovery of M. hominis from a brain abscess associated with a postpartum infection. Seroconversion to the isolated strain was detected by both a metabolic inhibition test and an immunoblotting assay. This case demonstrates the pathogenic potential of M. hominis and the need for rapid recognition of the organism so that appropriate chemotherapeutic intervention can occur.

Ureaplasma urealyticum is a commensal organism of the lower genital tract of females, but in a subpopulation of individuals, it can invade the upper genital tract. It is a significant cause of chorioamnionitis and neonatal morbidity and mortality. There are 14 recognized serovars of U. urealyticum; these can be divided into two distinct clusters or biovars. Biovar 1 is composed of serovars 1, 3, 6, and 14, Biovar 2 is composed of serovars 2, 4, 5, 7, 8, 9, 10, 11, 12, and 13. We previously identified a surface antigen, the multiple-banded (MB) antigen, which contains both serovar-specific and cross-reactive epitopes. Genotypic characterization of the C-terminal region of the MB antigen of serovar 3 indicates that serovar specificity and MB antigen size variation reside in that domain. In the present study, we used PCR analysis with primers derived from the serovar 3 MB antigen gene DNA sequence to determine if the MB antigen gene was present in the remaining 13 reference serovars as well as in invasive clinical isolates. The results indicated that not only was the MB antigen gene present in all serovars but that the genes' 5' regions were markers of biovar specificity and diversity. Further analysis of this region should reveal the phylogenetic relationship among serovars of U. urealyticum and, possibly, their invasive potential.