Invasive Community-Onset Gram-Positive Infections From July 2018 Through December 2022 at 2 Children's Hospitals.

Background: Invasive infections caused by Streptococcus pyogenes (invasive group A streptococcus [iGAS]) and Streptococcus pneumoniae (invasive pneumococcal disease [IPD]) decreased substantially at the beginning of the COVID-19 pandemic. Our study sought to evaluate the extent of this decrease and the trends of these infections since reversion of societal adjustments incident to the pandemic. We also wanted to compare the frequency of these infections with invasive community-onset Staphylococcus aureus (I-CO-SA) infections and common respiratory viral infections in this period. Methods: Cases of iGAS, IPD, and I-CO-SA infections were identified prospectively and retrospectively at 2 large US children's hospitals by positive cultures from July 2018 through December 2022. Admission data were used to estimate frequency. For comparison, rates of respiratory syncytial virus (RSV), influenza, and SARS-CoV-2 were estimated by the number of positive viral test results at each institution. Results: I-CO-SA infections showed little variation in the study period. Rates of iGAS infection and IPD decreased by 46% and 44%, respectively, from 2019 to 2020, coinciding with a substantial decrease in RSV and influenza. In 2022, RSV and influenza infection rates increased to prepandemic winter season rates, coinciding with a return to prepandemic rates of IPD (225% increase from 2021 to 2022) and a surge above prepandemic rates of iGAS infections (543% increase from 2021 to 2022). Conclusions: The COVID-19 pandemic had an unexpected influence on IPD and iGAS infections that was temporally related to changes in rates of viral infections.

Multi-center clinical evaluation of the Panther Fusion SARS-CoV-2/Flu A/B/RSV assay in nasopharyngeal swab specimens from symptomatic individuals.

The symptomology is overlapping for respiratory infections due to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), influenza A/B viruses, and respiratory syncytial virus (RSV). Accurate detection is essential for proper medical management decisions. This study evaluated the clinical performance of the Panther Fusion SARS-CoV-2/Flu A/B/RSV assay in nasopharyngeal swab (NPS) specimens from individuals of all ages with signs and symptoms of respiratory infection consistent with COVID-19, influenza, or RSV. Retrospective known-positive and prospectively obtained residual NPS specimens were collected during two respiratory seasons in the USA. Clinical performance was established by comparing Panther Fusion SARS-CoV-2/Flu assay results to a three-molecular assay composite comparator interpretation for SARS-CoV-2 and to the FDA-cleared Panther Fusion Flu A/B/RSV assay results for all non-SARS-CoV-2 targets. A total of 1,900 prospective and 95 retrospective NPS specimens were included in the analyses. The overall prevalence in prospectively obtained specimens was 20.7% for SARS-CoV-2, 6.7% for influenza A, and 0.7% for RSV; all influenza B-positive specimens were retrospective specimens. The positive percent agreement of the Panther Fusion assay was 96.9% (378/390) for SARS-CoV-2, 98.0% (121/123) for influenza A virus, 95.2% (20/21) for influenza B virus, and 96.6% (57/59) for RSV. The negative percent agreement was ≥98.5% for all target viruses. Specimens with discordant Panther Fusion SARS/Flu/RSV assay results all had cycle threshold values of ≥32.4 (by comparator or by Panther Fusion SARS/Flu/RSV assay). Only five co-infections were detected in the study specimens. The Panther Fusion SARS-CoV-2/Flu/RSV assay provides highly sensitive and specific detection of SARS-CoV-2, influenza A virus, influenza B virus, and RSV in NPS specimens.

Comparison of Bruker Biotyper® and Vitek® MS matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry platforms for the identification of filamentous fungi.

Aims: To evaluate the performance of two matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry platforms to identify molds isolated from clinical specimens. Methods: Fifty mold isolates were analyzed on Bruker Biotyper® and Vitek® MS platforms. Two Bruker Biotyper extraction protocols were assessed alongside the US FDA-approved extraction protocol for Vitek MS. Results: The Bruker Biotyper modified NIH-developed extraction protocol correctly identified more isolates than Bruker's protocol (56 vs 33%). For species in the manufacturers' databases, Vitek MS correctly identified 85% of isolates, with 8% misidentifications. The Bruker Biotyper identified 64%, with no misidentifications. For isolates not in the databases, the Bruker Biotyper did not misidentify any, and Vitek MS misidentified 36%. Conclusion: Both the Vitek MS and Bruker Biotyper accurately identified the fungal isolates, however Vitek MS was more likely to misidentify isolates than the Bruker Biotyper.

There are two different mass spectrometry systems that can be used in the hospital laboratory to find out what kind of mold is growing from a patient sample: the Vitek^® MS and Bruker Biotyper^® systems. This study compared how well they work for mold identification and also looked at two different ways to prepare the mold for testing. The Vitek MS system identified more molds, but also made more mistakes when identifying them. The Bruker Biotyper identified fewer molds but did not make any mistakes on the identification. The Vitek MS system sometimes gets the type of mold wrong, so more tests may be needed to be sure of the result. The Bruker Biotyper is more accurate because it got all of the molds correct, but it could not identify as many.

Multicenter Evaluation of the DiaSorin Molecular Simplexa Congenital CMV Direct PCR Test on Neonatal Saliva and Urine Specimens.

Cytomegalovirus (CMV) is the most common virus associated with congenital infection worldwide and is a major cause of sensorineural hearing loss (SNHL) and developmental delay. Up to 90% of infants with congenital CMV (cCMV) infection are asymptomatic at birth, making the diagnosis challenging. Postnatal diagnosis involves testing newborn saliva and/or urine collected before 21 days of life to confirm cCMV infection. This multicenter study evaluated the performance of the Simplexa Congenital CMV Direct real-time PCR assay for the qualitative detection of CMV in newborn saliva (n = 2,023) and urine (n = 1,797) specimens. Compared to two PCR/bidirectional sequencing assays, the Simplexa Congenital CMV Direct assay demonstrated positive percent agreement (PPA) and negative percent agreement (NPA) of 98.6% and 99.9%, respectively, for saliva samples and a PPA of 97.8% and an NPA of 99.9% for urine specimens. Overall concordance was κ = 0.98 or near perfect compared to the composite reference methods with both sample types. By 95% probit analysis, the limit of detection (LoD) using the AD-169 reference strain was 350 ± 12 copies/mL in urine. The LoDs of saliva swabs in either 1 mL or 3 mL of transport medium were 274 ± 12 copies/mL and 300 ± 14 copies/mL, respectively. The Simplexa Congenital CMV Direct assay can be applied to both saliva and urine specimens collected from newborns less than 21 days of age to rapidly and reliably identify CMV infection.

Acute liver failure and unique challenges of pediatric liver transplantation amidst a worldwide cluster of adenovirus-associated hepatitis.

Investigation into a recent cluster of acute hepatitis in children from the southeastern United States identified human adenovirus (HAdV) DNAemia in all 9 cases. Molecular genotyping in 5 of 9 (56%) children identified HAdV type 41 in all cases (100%). Importantly, 2 children from this cluster progressed rapidly to pediatric acute liver failure (PALF) and required liver transplantation. HAdV type 41, a known cause of self-limited gastroenteritis, has not previously been associated with severe cholestatic hepatitis and liver failure in healthy children. Adenovirus polymerase chain reaction assay and sequencing of amplicons performed on DNA extracted from formalin-fixed, paraffin-embedded liver tissue also identified adenovirus species F (HAdV type 40 or 41) in these 2 children with PALF. Transplant considerations and successful liver transplantation in such situations remain scarce. In this report, we describe the clinical course, laboratory results, liver pathology, and treatment of 2 children with PALF associated with HAdV type 41, one of whom developed secondary hemophagocytic lymphohistiocytosis. Their successful posttransplant outcomes demonstrate the importance of early multidisciplinary medical management and the feasibility of liver transplantation in some children with PALF and HAdV DNAemia.

Screening pediatric surgical patients during the COVID-19 pandemic.

ABSTRACT: SARS-CoV-2 has profoundly affected the way healthcare is delivered and has created significant strain on medical facilities globally. As a result, hospitals have had to continuously adapt in order to provide optimal patient care while minimizing the risk of SARS-CoV-2 transmission, particularly in the surgical setting. Texas Children's Hospital developed a set of protocols for surgical screening and clearance of patients in the context of the COVID-19 pandemic. These screening protocols were designed to mitigate the risk of exposing patients and healthcare providers to SARS-CoV-2 and have evolved significantly as a result of the emerging changes in medicine, technology, and governmental regulations. In this article, we share the reasoning behind the development, implementation, and successive modification of our institutional screening protocols.

Molecular Epidemiology of Contemporary Invasive Haemophilus influenzae Isolates in Texas Children.

Although vaccination has reduced the incidence of Haemophilus influenzae type b, nontypeable H. influenzae and other encapsulated types remain a health threat. Little is known regarding the contemporary molecular epidemiology of these organisms. We conducted multilocus sequence typing on invasive H. influenzae during a period of increasing incidence.

Comparison of Mid-Turbinate and Nasopharyngeal Specimens for Molecular Detection of SARS-CoV-2 Among Symptomatic Outpatients at a Pediatric Drive-Through Testing Site.

BACKGROUND: Nasopharyngeal (NP) specimen testing by reverse transcriptase polymerase chain reaction (RT-PCR) is the standard of care for detecting SARS-CoV-2. Data comparing the sensitivity and specificity of the NP specimen to the less invasive, mid-turbinate (MT) nasal specimen in children are limited. METHODS: Paired clinical NP and research MT specimens were collected from children <18 years with respiratory symptoms and tested by molecular assays to detect SARS-CoV-2 RNA. Sensitivity, specificity, and agreement (Cohen's kappa [κ]) were calculated for research MT specimens compared to the clinical NP specimens. RESULTS: Out of 907 children, 569 (62.7%) had parental consent and child assent when appropriate to participate and provided paired MT and NP specimens a median of 4 days after symptom onset (range 1-14 days). 16.5% (n = 94) of MT specimens were positive for SARS-CoV-2 compared with 20.0% (n = 114) of NP specimens. The sensitivity of research MT compared to clinical NP specimens was 82.5% (95% CI: 74.2%, 88.9%), specificity was 100.0% (95% CI: 99.2%, 100.0%), and overall agreement was 96.1% (κ = 0.87). The sensitivity of MT specimens decreased with time from 100% (95% CI: 59.0%, 100.0%) on day 1 of illness to 82.1% (95% CI: 73.8%, 88.7%) within 14 days of illness onset; sensitivity was generally >90% when specimens were collected within the first week of illness. CONCLUSION: MT specimens, particularly those collected within the first week of illness, have moderately reduced sensitivity and equivalent specificity to less-tolerated NP specimens in pediatric outpatients. MT specimen use in children may represent a viable alternative to NP specimen collection.

Retrospective analysis of infection and antimicrobial resistance patterns of Mycoplasma genitalium among pregnant women in the southwestern USA.

BACKGROUND: Mycoplasma genitalium is a sexually transmitted infection (STI) pathogen. There have been no published studies concerning symptomatology, prevalence data, antibiotic resistance profiling or reports of co-infection with other STI in pregnant women. OBJECTIVE: To describe these characteristics among pregnant women attending prenatal clinics in a large tertiary care centre. DESIGN: Remnant genital samples collected from pregnant women between August 2018 and November 2019 were tested for M. genitalium and Trichomonas vaginalis by the transcription-mediated amplification technique. Specimens with detectable M. genitalium RNA were sequenced for 23S rRNA mutations associated with azithromycin resistance and parC and gyrA mutations associated with resistance to moxifloxacin. Demographic, obstetric and STI co-infection data were recorded. RESULTS: Of the 719 samples, 41 (5.7 %) were positive for M. genitalium. M. genitalium infection was associated with black race, Hispanic ethnicity and young age (p=0.003, p=0.008 and p=0.004, respectively). M. genitalium infection was also associated with T. vaginalis co-infection and Streptococcus agalactiae (group B Streptococcus) colonisation (p≤0.001 and p=0.002, respectively). Of the 41 positive samples, 26 (63.4%) underwent successful sequencing. Eight (30.8%) had 23S rRNA mutations related to azithromycin resistance. One of 26 (3.8%) positive samples with sequencing results had the gyrA gene mutation and 1 of 18 sequenced samples (5.6%) had the parC gene mutation associated with moxifloxacin resistance. CONCLUSIONS: Prevalence rates of M. genitalium in pregnant women was 5.7%. M. genitalium infection disproportionately affects young black women co-infected with T. vaginalis. Pregnant women remain at risk for persistent infection with M. genitalium due to decreased azithromycin susceptibility.

Performance of six SARS-CoV-2 RNA detection systems in symptomatic and asymptomatic pediatric and maternal patients.

Aim: This study evaluated the real-world performance of six test systems for detection of SARS-CoV-2 in 138 pediatric and 110 adult maternal patients. Materials & methods: Nasopharyngeal swabs were tested directly using the Aptima™ SARS-CoV-2 (Aptima) and Simplexa™ COVID-19 Direct (Simplexa), and with Altona RealStar® RT-PCR and CDC RT-PCR with nucleic acid extracted on the Roche® MagNA Pure 96 (Altona-MP96) or bioMérieux EMAG® (Altona-EMAG). Results/Conclusion: Overall percent-positive and percent-negative agreements among the six test systems were, respectively: Aptima: 94.8 and 100%; Altona-MP96: 96.5 and 99.3%; CDC-MP96: 100 and 99.3%; Altona-EMAG: 86.1 and 100%; CDC-EMAG: 98.2 and 100%; Simplexa: 87 and 99.2%. The six test systems showed agreement ranging from 92.7 (κ = 0.85) to 98.8% (κ = 0.98).

Update in Pediatric Diagnostic Microbiology.

Infants and young children are uniquely susceptible to primary viral and bacterial infections, predisposing them to responses of greater frequency and severity than in adults. Etiologies and manifestations of infections in pediatric patients are often different than those in adults. It can be challenging for clinical laboratories to implement appropriate microbiologic methods for rapid and accurate diagnoses in this population. Laboratorians should be cognizant of the distinctive features of children to provide comprehensive pediatric clinical microbiology services. This article discusses laboratory aspects of several clinically significant pediatric pathogens that cause severe harm to patients and impact public health responses.

Tracheal colonization factor A (TcfA) is a biomarker for rapid and specific detection of Bordetella pertussis.

Pertussis is a highly contagious disease for which prompt, point-of-care diagnosis remains an unmet clinical need. Results from conventional test modalities (nucleic acid detection, serology, and culture) take hours to days. To overcome this challenge, we identified a new biomarker (tracheal colonization factor A, TcfA) for detection of Bordetella pertussis infection by lateral flow immunoassay (LFIA). We developed a library of 28 epitope-mapped monoclonal antibodies against TcfA and incorporated three antibodies into a LFIA. The LFIA did not cross-react with common bacterial or fungal organisms, but did react with nine distinct B. pertussis strains. The minimal linear epitope sequences targeted by the LFIA were conserved in 98% of 954 B. pertussis isolates collected across 12 countries from 1949-2017. The LFIA's limit of detection was 3.0 × 105 CFU/mL with B. pertussis cells in buffer, 6.2 × 105 CFU/mL with nasopharyngeal washes from a non-human primate model, and 2.3 ng/mL with recombinant TcfA. The LFIA reacted with patient nasopharyngeal swab specimens containing as few as 1.8 × 106 B. pertussis genomes/mL and showed no false-positives. Rapid (< 20 min) LFIA detection of TcfA as a biomarker for B. pertussis infection is feasible and may facilitate early detection of pertussis.

Complications of Otitis Media and Sinusitis Caused by Streptococcus anginosus Group Organisms in Children.

BACKGROUND: The Streptococcus anginosus group (SAG, S. anginosus, S. intermedius and S. constellatus) are often associated with severe disease and abscess formation. In our institution, we observed an apparent increase in frequency of intraorbital and intracranial infections resulting from SAG at Texas Children's Hospital. We undertook a retrospective review to describe the frequency and clinical features of these infections. METHODS: We reviewed the database of the microbiology laboratory at Texas Children's Hospital from 2011 to 2018 for SAG-positive cultures. Cases included were those associated with (1) either otitis media or sinusitis and (2) Pott's puffy tumor, orbital abscesses, mastoiditis, epidural abscesses, subdural empyema, brain parenchymal abscesses or dural enhancement by imaging. The number of overall diagnoses were determined using diagnostic codes and used to estimate the proportion of disease caused by SAG. RESULTS: Ninety-five cases were identified meeting inclusion criteria. The median age of patients was 11.4 years, and 75.8% were previously healthy. S. intermedius was most commonly isolated (80%) followed by S. constellatus (12.6%) and S. anginosus (7.4%); 50.5% of cases were polymicrobial. Among polymicrobial cases, Staphylococcus aureus was most frequently isolated. All patients underwent surgical intervention. 8.4% of patients experienced persistent neurologic deficits. We observed a significant increase in disease incidence during the study period; in addition, the overall proportion of all intracranial infections caused by SAG increased. CONCLUSIONS: Complications of otitis media and sinusitis caused by SAG are associated with substantial morbidity. These infections are becoming increasingly common at our center although the precise reason for this temporal trend is unclear.

Invasive Haemophilus influenzae Disease at Texas Children's Hospital, 2011 to 2018.

BACKGROUND: Universal vaccination with Haemophilus influenzae type b conjugate vaccines has significantly changed the epidemiology of invasive H. influenzae disease in the United States. We reviewed the epidemiology, clinical features, and outcomes in 61 patients with invasive H. influenzae disease evaluated at Texas Children's Hospital (TCH). METHODS: Cases of invasive H. influenzae disease, defined as isolation of the organism from cerebrospinal fluid, blood, synovial fluid or pleural fluid, during 2011 to 2018 among children cared for at TCH in Houston, TX, were included. RESULTS: We identified 61 cases of invasive H. influenzae disease in children ≤18 years of age. The overall hospitalization rate due to invasive H. influenzae disease increased between 2011 and 2018 (0 vs. 0.64/1000 hospitalizations; P = 0.019). The majority (80%) of infections occurred in children <5 years of age. Of the 61 H. influenzae infections, 24 (39.3%) infections were caused by nontypeable H. influenzae strains, 18 (29.5%) infections were caused by H. influenzae type a, 12 (19.7%) infections were caused by H. influenzae type f, 3 (4.9%) infections were caused by H. influenzae type e and 4 (6.6%) isolates were not typed. A total of 78.7% of the isolates were ß-lactamase negative. The most common clinical presentations were bacteremia without a source, pneumonia and meningitis. CONCLUSIONS: The hospitalization rate for H. influenzae invasive disease increased over an 8-year period at TCH. The overall trend was mainly driven by an increasing number of invasive infections caused by nontypeable H. influenzae and H. influenzae type a. Morbidity was substantial, especially in meningitis cases.

CLIA-waived molecular influenza testing in the emergency department and outpatient settings.

Respiratory tract infections are a common cause of visits to emergency departments and outpatient settings. Infections with influenza viruses A and B in particular, are responsible for significant morbidity and mortality in both pediatric and adult populations worldwide. A significant number of influenza diagnoses occur in the emergency departments with many being performed using rapid influenza diagnostic tests (RIDT) which have sensitivities as low as 30% depending on the specific RIDT and patient population. More recently, rapid molecular tests for the detection of influenza viruses A and B have become commercially available as point-of-care platforms. In the United States, several of these new tests are approved by the Food and Drug Administration as CLIA-waived tests. In this report, we review the data on the analytical and clinical performance of RIDTs and CLIA-waived molecular tests, present and discuss potential key challenges and opportunities for implementation of CLIA-waived molecular tests at or near point of care in the emergency departments and outpatient settings.

The prevalence of antiseptic tolerance genes among staphylococci and enterococci in a pediatric population.

OBJECTIVE: The smr and qacA/B genes in Staphylococcus aureus confer tolerance to antiseptics and are associated with nosocomial acquisition of infection and underlying medical conditions. Such antiseptic tolerance (AT) genes have also been reported in coagulase-negative staphylococci (CoNS) and enterococci, however, few data are available regarding their prevalence. We sought to describe the frequency of AT genes among bloodstream isolates of S. aureus, CoNS and enterococci at Texas Children's Hospital (TCH). METHODS: Banked CoNS, S. aureus and enterococci isolated from blood cultures collected bewteen October 1, 2016, and October 1, 2017, were obtained from the TCH clinical microbiology laboratory. All isolates underwent polymerase chain reaction (PCR) assay for the qacA/B and smr genes. Medical records were reviewed for all cases. RESULTS: In total, 103 CoNS, 19 Enterococcus spp, and 119 S. aureus isolates were included in the study, and 80.6% of the CoNS possessed at least 1 AT gene compared to 37% of S. aureus and 43.8% of E. faecalis isolates (P < .001). Among CoNS bloodstream isolates, the presence of either AT gene was strongly associated with nosocomial infection (P < .001). The AT genes in S. aureus were associated with nosocomial infection (P = .025) as well as the diagnosis of central-line-associated bloodstream infection (CLABSI; P = .04) and recent hospitalizations (P < .001). We found no correlation with genotypic AT in E. faecalis and any clinical variable we examined. CONCLUSIONS: Antiseptic tolerance is common among bloodstream staphylococci and E. faecalis isolates at TCH. Among CoNS, the presence of AT genes is strongly correlated with nosocomial acquisition of infection, consistent with previous studies in S. aureus. These data suggest that the healthcare environment contributes to AT among staphylococci.

An Outbreak of Burkholderia cepacia Complex Infections Associated with Contaminated Liquid Docusate.

OBJECTIVE To investigate an outbreak of Burkholderia cepacia complex and describe the measures that revealed the source. SETTING A 629-bed, tertiary-care, pediatric hospital in Houston, Texas. PATIENTS Pediatric patients without cystic fibrosis (CF) hospitalized in the pediatric and cardiovascular intensive care units. METHODS We investigated an outbreak of B. cepacia complex from February through July 2016. Isolates were evaluated for molecular relatedness with repetitive extragenic palindromic polymerase chain reaction (rep-PCR); specific species identification and genotyping were performed at an independent laboratory. The investigation included a detailed review of all cases, direct observation of clinical practices, and respiratory surveillance cultures. Environmental and product cultures were performed at an accredited reference environmental microbiology laboratory. RESULTS Overall, 18 respiratory tract cultures, 5 blood cultures, 4 urine cultures, and 3 stool cultures were positive in 24 patients. Among the 24 patients, 17 had symptomatic infections and 7 were colonized. The median age of the patients was 22.5 months (range, 2-148 months). Rep-PCR typing showed that 21 of 24 cases represented the same strain, which was identified as a novel species within the B. cepacia complex. Product cultures of liquid docusate were positive with an identical strain of B. cepacia complex. Local and state health departments, as well as the CDC and FDA, were notified, prompting a multistate investigation. CONCLUSIONS Our investigation revealed an outbreak of a unique strain of B. cepacia complex isolated in clinical specimens from non-CF pediatric patients and from liquid docusate. This resulted in a national alert and voluntary recall by the manufacturer. Infect Control Hosp Epidemiol 2017;38:567-573.