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Background: Stenotrophomonas maltophilia is an important cause of opportunistic healthcare-associated infections (HAIs) in critically ill patients and is difficult to treat due to intrinsic resistance to multiple antibiotic classes. During the COVID-19 pandemic, the CDC received anecdotal reports of increases in S. maltophilia respiratory infections. To further investigate these reports, we used a national electronic healthcare database to evaluate changes in S. maltophilia during the pandemic. Methods: Using the PINC-AI healthcare data (Premier Inc, Charlotte, NC) we identified all potential HAIs by calculating the total number of unique patients hospitalized during January 1, 2018, through December 31, 2021, who had any organism isolated on clinical culture obtained >3 days after admission. We calculated the proportion of patients with S. maltophilia detected in culture and stratified them by specimen source. To determine whether COVID-19 diagnosis influenced the proportion of patients diagnosed with S. maltophilia respiratory infections during the pandemic (January 1, 2020–December 31, 2021), we calculated the proportion of patients with S. maltophilia detected among those with any bacterial pathogen isolated from a respiratory culture >3 days after hospitalization. We stratified these results by presence or absence of concurrent COVID-19 diagnosis. Pearson χ2 test was used to test for differences where appropriate. Results: Among hospitalized patients with any organism isolated from a clinical culture, the proportion with S. maltophilia detected was higher in 2021 (n = 2,554 of 118,029, 2.2%) than in 2018 (n = 2,063 of 155,624, 1.3%) p 3 days after hospital admission from 2018 to 2021. Most patient isolates were from respiratory specimens. A concurrent diagnosis of COVID-19 did not appear to increase the likelihood of respiratory S. maltophilia detection. The increases in S. maltophilia during the pandemic might be explained by challenges inherent to caring for increased numbers of higher-acuity patients during this time, including staffing shortages and changes to infection prevention practices. Additional exploration of these data, as well as data from other sources and from additional years, may help to elucidate this issue more fully.

Pseudomonas aeruginosa is intrinsically resistant to many antimicrobial drugs, making carbapenems crucial in clinical management. During July–October 2015 in the United States, we piloted laboratory-based surveillance for carbapenem-resistant P. aeruginosa (CRPA) at sentinel facilities in Georgia, New Mexico, Oregon, and Tennessee, and population-based surveillance in Monroe County, NY. An incident case was the first P. aeruginosa isolate resistant to antipseudomonal carbapenems from a patient in a 30-day period from any source except the nares, rectum or perirectal area, or feces. We found 294 incident cases among 274 patients. Cases were most commonly identified from respiratory sites (120/294; 40.8%) and urine (111/294; 37.8%); most (223/280; 79.6%) occurred in patients with healthcare facility inpatient stays in the prior year. Genes encoding carbapenemases were identified in 3 (2.3%) of 129 isolates tested. The burden of CRPA was high at facilities under surveillance, but carbapenemase-producing CRPA were rare.

ABSTRACT Antimicrobial resistance is a threat to public health globally and leads to an estimated 23,000 deaths annually in the United States alone. Here, we report the genomic characterization of an unusual Klebsiella pneumoniae, nonsusceptible to all 26 antibiotics tested, that was isolated from a U.S. patient. The isolate harbored four known beta-lactamase genes, including plasmid-mediated blaNDM-1 and blaCMY-6, as well as chromosomal blaCTX-M-15 and blaSHV-28, which accounted for resistance to all beta-lactams tested. In addition, sequence analysis identified mechanisms that could explain all other reported nonsusceptibility results, including nonsusceptibility to colistin, tigecycline, and chloramphenicol. Two plasmids, IncA/C2 and IncFIB, were closely related to mobile elements described previously and isolated from Gram-negative bacteria from China, Nepal, India, the United States, and Kenya, suggesting possible origins of the isolate and plasmids. This is one of the first K. pneumoniae isolates in the United States to have been reported to the Centers for Disease Control and Prevention (CDC) as nonsusceptible to all drugs tested, including all beta-lactams, colistin, and tigecycline. IMPORTANCE Antimicrobial resistance is a major public health threat worldwide. Bacteria that are nonsusceptible or resistant to all antimicrobials available are of major concern to patients and the public because of lack of treatment options and potential for spread. A Klebsiella pneumoniae strain that was nonsusceptible to all tested antibiotics was isolated from a U.S. patient. Mechanisms that could explain all observed phenotypic antimicrobial resistance phenotypes, including resistance to colistin and beta-lactams, were identified through whole-genome sequencing. The large variety of resistance determinants identified demonstrates the usefulness of whole-genome sequencing for detecting these genes in an outbreak response. Sequencing of isolates with rare and unusual phenotypes can provide information on how these extremely resistant isolates develop, including whether resistance is acquired on mobile elements or accumulated through chromosomal mutations. Moreover, this provides further insight into not only detecting these highly resistant organisms but also preventing their spread.