The role of plasmids in carbapenem resistant E. coli in Alameda County, California.

BACKGROUND: Antimicrobial resistant infections continue to be a leading global public health crisis. Mobile genetic elements, such as plasmids, have been shown to play a major role in the dissemination of antimicrobial resistance (AMR) genes. Despite its ongoing threat to human health, surveillance of AMR in the United States is often limited to phenotypic resistance. Genomic analyses are important to better understand the underlying resistance mechanisms, assess risk, and implement appropriate prevention strategies. This study aimed to investigate the extent of plasmid mediated antimicrobial resistance that can be inferred from short read sequences of carbapenem resistant E. coli (CR-Ec) in Alameda County, California. E. coli isolates from healthcare locations in Alameda County were sequenced using an Illumina MiSeq and assembled with Unicycler. Genomes were categorized according to predefined multilocus sequence typing (MLST) and core genome multilocus sequence typing (cgMLST) schemes. Resistance genes were identified and corresponding contigs were predicted to be plasmid-borne or chromosome-borne using two bioinformatic tools (MOB-suite and mlplasmids). RESULTS: Among 82 of CR-Ec identified between 2017 and 2019, twenty-five sequence types (STs) were detected. ST131 was the most prominent (n = 17) followed closely by ST405 (n = 12). blaCTX-M were the most common ESBL genes and just over half (18/30) of these genes were predicted to be plasmid-borne by both MOB-suite and mlplasmids. Three genetically related groups of E. coli isolates were identified with cgMLST. One of the groups contained an isolate with a chromosome-borne blaCTX-M-15 gene and an isolate with a plasmid-borne blaCTX-M-15 gene. CONCLUSIONS: This study provides insights into the dominant clonal groups driving carbapenem resistant E. coli infections in Alameda County, CA, USA clinical sites and highlights the relevance of whole-genome sequencing in routine local genomic surveillance. The finding of multi-drug resistant plasmids harboring high-risk resistance genes is of concern as it indicates a risk of dissemination to previously susceptible clonal groups, potentially complicating clinical and public health intervention.

Clonal Lineages and Virulence Factors of Carbapenem Resistant E. coli in Alameda County, California, 2017-2019.

The prevalence of carbapenem-resistant Enterobacterales (CRE) has been increasing since the year 2000 and is considered a serious public health threat according to the Centers for Disease Control and Prevention. Limited studies have genotyped Carbapenem-resistant Escherichia coli using whole genome sequencing to characterize the most common lineages and resistance and virulence genes. The aim of this study was to characterize sequence data from carbapenem-resistant E. coli isolates (n = 82) collected longitudinally by the Alameda County Public Health Laboratory (ACPHL) between 2017 and 2019. E. coli genomes were screened for antibiotic resistance genes (ARGs) and extraintestinal pathogenic E. coli virulence factor genes (VFGs). The carbapenem-resistant E. coli lineages were diverse, with 24 distinct sequence types (STs) represented, including clinically important STs: ST131, ST69, ST95, and ST73. All Ambler classes of Carbapenemases were present, with NDM-5 being most the frequently detected. Nearly all isolates (90%) contained genes encoding resistance to third-generation cephalosporins; blaCTX-M genes were most common. The number of virulence genes present within pandemic STs was significantly higher than the number in non-pandemic lineages (p = 0.035). Virulence genes fimA (92%), trat (71%), kpsM (54%), and iutA (46%) were the most prevalent within the isolates. Considering the public health risk associated with CRE, these data enhance our understanding of the diversity of clinically important E. coli that are circulating in Alameda County, California.

Assessing the Use of PCR To Screen for Shedding of Salmonella enterica in Infected Humans.

Recovery from enteric bacterial illness often includes a phase of organismal shedding over a period of days to months. The monitoring of this process through laboratory testing forms the foundation of public health action to prevent further transmission. Regulations in most jurisdictions in the United States exclude individuals who continue to shed certain organisms from sensitive occupations and situations, such as food handling, providing direct patient care, or attending day care. The burden that this creates for recovering patients and their families/coworkers is great, so any effort to provide efficiency to the testing process would be of significant benefit. We sought to assess the ability of PCR for the detection of Salmonella enterica shedding and to compare that ability to culture-based testing. PCR would be faster than culture and would allow results to be generated more quickly. Herein, we show data that indicate that, while PCR and culture testing agree in the majority of cases, there are incidents of discordance between the two tests, whereupon PCR shows positive results when culture indicates lack of detectable viable organisms. Using culture-based testing as the standard, the negative predictive value of PCR was found to be 100%, while the positive predictive value was 79%. The nature of this discordance is briefly investigated. We found that it is possible that PCR may not only detect nonviable organisms in stool but also viable organisms that remain undetectable by standard culture methods.

An independent effectiveness trial of multisystemic therapy with juvenile justice youth.

This study examines the effectiveness of an evidence-based practice, multisystemic therapy (MST), conducted in a real-world mental health setting with juvenile justice involved youth and their families. Importantly, this is the first randomized clinical trial of MST with juvenile offenders in the United States conducted without direct oversight by the model developers. This study reports outcomes achieved for 93 youth randomly assigned to MST or treatment as usual (TAU) services through 18-month follow-up posttreatment for offense data and 6-month follow-up posttreatment for ratings of the Child and Adolescent Functional Assessment Scale (CAFAS). Outcomes include significant reduction in rearrest and improvement in 4 areas of functioning measured by the CAFAS for youth who received MST. Implications for delivery of empirically supported treatments in real-world settings are discussed.