Mycoplasma pneumoniae Outbreak in 2023: Post-pandemic Resurgence of an Atypical Bacterial Pathogen.

The syndromic nature of infections caused by pneumonia-causing pathogens including Mycoplasma pneumoniae necessitates detection via multiplex PCR for accurate and timely diagnosis to control the infection spread. In this study, we demonstrate an increase in the detection of M. pneumoniae in the outpatient population, during 2023, as compared to the previous two years (2021-2022). In this aggregated survey, respiratory samples collected within the continental United States were tested for the presence of M. pneumoniae and other respiratory bacterial and viral pathogens using a multiplex PCR assay. Patient data was analyzed on the basis of age, gender and geographical location. The positive detection of M. pneumoniae in 2021 and 2022 was 0.004% and 0.006%, respectively. The positivity rate of M. pneumoniae in 2023 increased to 0.21%. The highest proportion of M. pneumoniae cases were detected from Georgia with the outbreak generally concentrated in large urban settings. Median age of the patients testing positive for M. pneumoniae was 10 (interquartile range [IQR] 8-18) years with an almost equal distribution between male and female patients. Other respiratory, viral and bacterial, pathogens detected in samples positive for M. pneumoniae were similar in proportion to the M. pneumonia-negative population. A survey of the ICD-10 codes submitted in conjunction with the samples suggests that the current outbreak is mostly associated with upper respiratory tract infections. The present study is the first detailed report in the United States that shows an unprecedented increase in the detection of M. pneumoniae in the outpatient population during 2023. Our analysis suggests that this outbreak was not associated with any other bacterial or viral respiratory pathogen. The outbreak of this atypical pathogen was concentrated in the pediatric population in large urban areas. The 2023 outbreak could be a return of the cyclical M. pneumoniae outbreaks witnessed prior to the COVID-19 pandemic. Our study highlights the importance of performing continuous surveillance of respiratory pathogens, especially in the altered epidemiological landscape of the post-COVID world.

Prevalence of Undiagnosed Monkeypox Virus Infections during Global Mpox Outbreak, United States, June-September 2022.

Since May 2022, mpox has been identified in 108 countries without endemic disease; most cases have been in gay, bisexual, or other men who have sex with men. To determine number of missed cases, we conducted 2 studies during June-September 2022: a prospective serologic survey detecting orthopoxvirus antibodies among men who have sex with men in San Francisco, California, and a retrospective monkeypox virus PCR testing of swab specimens submitted for other infectious disease testing among all patients across the United States. The serosurvey of 225 participants (median age 34 years) detected 18 (8.0%) who were orthopoxvirus IgG positive and 3 (1.3%) who were also orthopoxvirus IgM positive. The retrospective PCR study of 1,196 patients (median age 30 years; 54.8% male) detected 67 (5.6%) specimens positive for monkeypox virus. There are likely few undiagnosed cases of mpox in regions where sexual healthcare is accessible and patient and clinician awareness about mpox is increased.

Expanded PCR Panel Testing for Identification of Respiratory Pathogens and Coinfections in Influenza-like Illness.

While COVID-19 has dominated Influenza-like illness (ILI) over the past few years, there are many other pathogens responsible for ILI. It is not uncommon to have coinfections with multiple pathogens in patients with ILI. The goal of this study was to identify the different organisms in symptomatic patients presenting with ILI using two different high throughput multiplex real time PCR platforms. Specimens were collected from 381 subjects presenting with ILI symptoms. All samples (nasal and nasopharyngeal swabs) were simultaneously tested on two expanded panel PCR platforms: Applied Biosystems™ TrueMark™ Respiratory Panel 2.0, OpenArray™ plate (OA) (32 viral and bacterial targets); and Applied Biosystems™ TrueMark™ Respiratory Panel 2.0, TaqMan™ Array card (TAC) (41 viral, fungal, and bacterial targets). Results were analyzed for concordance between the platforms and for identification of organisms responsible for the clinical presentation including possible coinfections. Very good agreement was observed between the two PCR platforms with 100% agreement for 12 viral and 3 bacterial pathogens. Of 381 specimens, approximately 58% of the samples showed the presence of at least one organism with an important incidence of co-infections (~36-40% of positive samples tested positive for two and more organisms). S. aureus was the most prevalent detected pathogen (~30%) followed by SARS-CoV-2 (~25%), Rhinovirus (~15%) and HHV6 (~10%). Co-infections between viruses and bacteria were the most common (~69%), followed by viral-viral (~23%) and bacterial-bacterial (~7%) co-infections. These results showed that coinfections are common in RTIs suggesting that syndromic panel based multiplex PCR tests could enable the identification of pathogens contributing to coinfections, help guide patient management thereby improving clinical outcomes and supporting antimicrobial stewardship.

SARS-CoV-2 respiratory co-infections: Incidence of viral and bacterial co-pathogens.

The global coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in an unprecedented challenge to our healthcare system. Secondary and concurrent bacterial and viral co-infections are well documented for other viral respiratory pathogens; however knowledge regarding co-infections in COVID-19 remains limited. In the present study, concurrent testing of 50 419 individual samples for the presence of SARS-CoV-2 and other bacterial and viral respiratory pathogens was performed between March and August 2020. Overall, a lower rate of viral co-infection was observed in the SARS-CoV-2-positive population when compared to the population testing negative for the virus. Significant levels of Staphylococcus aureus and Epstein-Barr virus co-infections were detected in the SARS-CoV-2-positive population. This is one of the largest surveys looking into the co-infection patterns of SARS-CoV-2 infection in the United States. Data from this study will enhance our understanding of the current pandemic and will assist clinicians in making better patient care decisions, especially with respect to antimicrobial therapy.