High Rates of Human Fecal Carriage of mcr-1–Positive Multidrug-Resistant Enterobacteriaceae Emerge in China in Association With Successful Plasmid Families

Background: mcr-1–mediated colistin resistance in Enterobacteriaceae is concerning, as colistin is used in treating multidrug-resistant Enterobacteriaceae infections. We identified trends in human fecal mcr-1-positivity rates and colonization with mcr-1–positive, third-generation cephalosporin-resistant (3GC-R) Enterobacteriaceae in Guangzhou, China, and investigated the genetic contexts of mcr-1 in mcr-1–positive 3GC-R strains. / Methods: Fecal samples were collected from in-/out-patients submitting specimens to 3 hospitals (2011–2016). mcr-1 carriage trends were assessed using iterative sequential regression. A subset of mcr-1–positive isolates was sequenced (whole-genome sequencing [WGS], Illumina), and genetic contexts (flanking regions, plasmids) of mcr-1 were characterized. / Results: Of 8022 fecal samples collected, 497 (6.2%) were mcr-1 positive, and 182 (2.3%) harbored mcr-1–positive 3GC-R Enterobacteriaceae. We observed marked increases in mcr-1 (0% [April 2011] to 31% [March 2016]) and more recent (since January 2014; 0% [April 2011] to 15% [March 2016]) increases in human colonization with mcr-1–positive 3GC-R Enterobacteriaceae (P < .001). mcr-1–positive 3GC-R isolates were commonly multidrug resistant. WGS of mcr-1–positive 3GC-R isolates (70 Escherichia coli, 3 Klebsiella pneumoniae) demonstrated bacterial strain diversity; mcr-1 in association with common plasmid backbones (IncI, IncHI2/HI2A, IncX4) and sometimes in multiple plasmids; frequent mcr-1 chromosomal integration; and high mobility of the mcr-1–associated insertion sequence ISApl1. Sequence data were consistent with plasmid spread among animal/human reservoirs. / Conclusions: The high prevalence of mcr-1 in multidrug-resistant E. coli colonizing humans is a clinical threat; diverse genetic mechanisms (strains/plasmids/insertion sequences) have contributed to the dissemination of mcr-1, and will facilitate its persistence

Using electronic health records to improve management of E. coli bloodstream infections

The aim of this thesis is to use linked electronic health records of hospital admissions, and microbiology and haematology results in order to inform management of infections in Oxfordshire, and more generally worldwide. Escherichia coli is one of the leading bacterial pathogens causing bloodstream infections; not only is overall incidence rising, but rising resistance to commonly used empiric antibiotics is also a major concern. Despite playing such a significant role in the burden of infections, the epidemiology of E. coli bloodstream infections is still unclear, particularly when considering unselected populations. I showed that the rise in E. coli bloodstream infections in Oxfordshire is driven by truly community-associated cases, that is, cases identified in the first 48 hours of a hospital admission, or outside of a hospital admission, who had not been admitted to the hospital in the past year. Interestingly, the rate of increase in incidence was faster the further away the previous hospital admission had been. However, rising incidence did not seem to be driven by increasing numbers of patients with evidence of a previous urinary tract infection. The number of co-amoxiclav resistant infections was rising significantly faster than the number of co-amoxiclav susceptible infections and the highest number of resistant infections in 2016 was seen in community-associated cases. However, considering 30-day mortality and various biomarkers of infection, there was no evidence for changes in the severity of infections over time. Higher co-amoxiclav use in primary care was associated with higher rates of co-amoxiclav resistant E. coli urinary tract infections in the subsequent year, providing the evidence needed in order to support the aim of lowering inappropriate use of broad-spectrum antibiotics in the community. Co-amoxiclav susceptibility is particularly challenging to define with traditional laboratory testing methods, with different methodologies leading to different results both in terms of minimum inhibitory concentrations, but particularly when considering a dichotomised susceptible/resistant phenotype. Recent advances in whole genome sequencing technology and analysis tools, as well as decreases in costs, increase the potential utility of predicting phenotype from sequencing-derived genotype, particularly for challenging bacteria-drug combinations. I found that machine learning algorithms – statistical methods which learn from patterns within the data without being programmed explicitly – could predict co-amoxiclav resistance where information is extracted from assembled sequences, either through extracting information about genetic features from mapping onto resistance databases or by considering presence and absence of DNA ‘words’ (k-mers). Crucially, feature selection and expert knowledge are not required when constructing these matrices of genetic features, making these algorithms particularly appealing when considering the constant accumulation of new genetic resistance mechanisms. Finally, by comparing the proportions of resistant bloodstream infections and infections in other less invasive sites, I found that the latter could be used as a surveillance tool for antimicrobial resistance in low- and middle-income countries, since these sites are easier to sample from and cheaper to carry out antimicrobial susceptibility testing on.</p

High rates of human fecal carriage of mcr-1-positive multi-drug resistant Enterobacteriaceae isolates emerge in China in association with successful plasmid families

Objectives mcr-1-mediated colistin resistance in Enterobacteriaceae is concerning, as colistin is used in treating multidrug-resistant Enterobacteriaceae infections. Rates of human mcr-1 gastrointestinal carriage have historically been low. We identified trends in human fecal mcr-1-positivity rates and colonization with mcr-1-positive+third-generation cephalosporin-resistant (3GC-R) Enterobacteriaceae in Guangzhou, China, and investigated the genetic contexts of mcr-1 in a subset of mcr-1-positive+3GC-R strains. Methods Fecal samples were collected from in-patients and out-patients submitting specimens to three hospitals (2011-2016). mcr-1 carriage trends were assessed using iterative sequential regression. A subset of mcr-1-positive isolates was sequenced (whole genome sequencing [WGS], Illumina), and genetic contexts (flanking regions, plasmids) of mcr-1 characterized. Results Of 8,022 fecal samples collected, 497 (6.2%) were mcr-1-positive, and 182 (2.3%) harbored mcr-1-positive+3GC-R Enterobacteriaceae. We observed marked increases in mcr-1 (0% [Apr/2011] to 31% [Mar/2016]) and more recent (since January 2014; 0% [Apr/2011] to 15% [Mar/2016]) increases in human colonization with mcr-1-positive+3GC-R Enterobacteriaceae (p&lt;0.001). mcr-1-positive+3GC-R isolates were commonly multi-drug resistant. WGS of mcr-1-positive+3GC-R isolates (70 Escherichia coli, 3 Klebsiella pneumoniae) demonstrated bacterial strain diversity (48 E. coli sequence types); mcr-1 in association with common plasmid backbones (IncI, IncHI2/HI2A, IncX4) and sometimes in multiple plasmids; frequent mcr-1 chromosomal integration; and high mobility of the mcr-1-associated insertion sequence ISApl1. Sequence similarity with published mcr-1 plasmid sequences was consistent with spread amongst animal/human reservoirs. Conclusions The high prevalence of mcr-1 in multidrug-resistant E. coli colonizing humans is a clinical threat; diverse genetic mechanisms (strains/plasmids/insertion sequences) have contributed to the dissemination of mcr-1, and will facilitate its persistence.</p