Emergence of diversity in carbapenemase-producing Escherichia coli ST131, England, January 2014 to June 2016

Colonization with resistant bacteria in hospital employees: an epidemiological surveillance and typing study

The objective of this study was to determine the prevalence, molecular epidemiology, and risk factors for gut colonization with extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E), carbapenemase-producing Enterobacterales (CPE), and vancomycin-resistant enterococci (VRE) in healthcare workers (HCWs). In September/October 2022, we performed a cross-sectional study among HCW from 14 institutions in Northeastern Switzerland. HCWs reported risk factors for antimicrobial resistance (covering the last 12-24 months) and provided rectal swabs. Swabs were screened for ESBL-E, CPE, and VRE; whole-genome sequencing (WGS) was performed to assess the genetic relatedness. Logistic regression was used to identify occupational and non-occupational risk factors. Among approximately 22,500 employees, 1,209 participated (median age 46 years, 82% female). Prevalences of ESBL-E (n = 65) and CPE (n = 1) were 5.4% [95% confidence interval (CI) 4.2-6.8] and 0.1% (95% CI 0.0-0.5), respectively; no VREs were detected. In the multivariable analysis, non-European ethnicity [adjusted odds ratio (aOR) 7.0, 95% CI 1.4-27.3], travel to high-risk countries (aOR 4.9, 95% CI 2.5-9.3), systemic antibiotics (aOR 2.1, 95% CI 1.1-3.7), antibiotic eye drops (aOR 4.7, 95% CI 1.7-11.9), and monthly sushi consumption (aOR 2.4, 95% CI 1.4-4.3) were positively associated with ESBL-E colonization, whereas alcohol consumption (aOR 0.5 per glass/week, 95% CI 0.3-0.9) was negatively associated with ESBL-E colonization. Occupational factors showed no association. Among ESBL-Escherichia coli, ST131 (15 of 61, 25%) and blaCTX-M-15 (37/61; 61%) were most common; one isolate co-harbored blaOXA-244. WGS data did not show relevant clustering. Occupational exposure is not associated with ESBL-E colonization in HCW. Given the potential public health and antibiotic stewardship implications, the role of sushi consumption and antibiotic eye drops as risk factors should be further elucidated.

International Epidemiology of Carbapenemase-Producing Escherichia coli

BACKGROUND

Carbapenemase-producing (CP) Escherichia coli (CP-Ec) are a global public health threat. We aimed to describe the clinical and molecular epidemiology and outcomes of patients from several countries with CP-Ec isolates obtained from a prospective cohort.

METHODS

Patients with CP-Ec were enrolled from 26 hospitals in 6 countries. Clinical data were collected, and isolates underwent whole-genome sequencing. Clinical and molecular features and outcomes associated with isolates with or without metallo-β-lactamases (MBLs) were compared. The primary outcome was desirability of outcome ranking (DOOR) at 30 days after the index culture.

RESULTS

Of the 114 CP-Ec isolates in Consortium on resistance against carbapenems in Klebsiella and other Enterobacterales-2 (CRACKLE-2), 49 harbored an MBL, most commonly blaNDM-5 (38/49, 78%). Strong regional variations were noted with MBL-Ec predominantly found among patients in China (23/49). Clinically, MBL-Ec were more often from urine sources (49% vs 29%), less often met criteria for infection (39% vs 58%, P = .04), and had lower acuity of illness when compared with non-MBL-Ec. Among patients with infection, the probability of a better DOOR outcome for a randomly selected patient with MBL-Ec as compared with non-MBL-Ec was 62% (95% CI: 48.2-74.3%). Among infected patients, non-MBL-Ec had increased 30-day (26% vs 0%; P = .02) and 90-day (39% vs 0%; P = .001) mortality compared with MBL-Ec.

CONCLUSIONS

Emergence of CP-Ec was observed with important geographic variations. Bacterial characteristics, clinical presentations, and outcomes differed between MBL-Ec and non-MBL-Ec. Mortality was higher among non-MBL isolates, which were more frequently isolated from blood, but these findings may be confounded by regional variations.

High Emergence of Multidrug-Resistant Sequence Type 131 Subclade C2 among Extended-Spectrum β-Lactamase (ESBL)-Producing Escherichia coli Isolated from the University Hospital Bratislava, Slovakia

The expansion of sequence type 131 (ST131) extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (E. coli) represents major worldwide challenges. E. coli strains originating from healthcare facilities (labeled No. 1 and No. 2) of the University Hospital Bratislava (UHB) were analyzed for ST131 emergence, including its (sub)lineages and clonal relatedness. Antimicrobial resistance was determined in most strains. Of a total of 354 E. coli strains, 263 (74.3%) belonged to ST131; of these, 177 (67.3%) were from No. 1. Generally, among 260 ST131 E. coli, clades A/B were confirmed in 20 (7.7%), while clade C was noted in 240 (92.3%) strains; within them, subclades were detected as follows: C0 (17; 7.1%), C1 (3; 1.2%), and C2 (220; 91.7%). Among fifteen randomly selected E. coli strains that were investigated for ST and clonal relatedness, seven STs were identified: eight (53.3%) ST131, two (13.3%) ST73, and one each (6.7%) of ST10, ST12, ST14, ST1193, and ST1196. From No. 1, two ST131 in the first internal clinic and one ST131 from No. 2 in the aftercare department were highly clonally related, suggesting possible epidemiological association. Antimicrobial resistance was as follows: ciprofloxacin 93.8%, ceftazidime 78.4%, meropenem 0%, fosfomycin 2.9% and nitrofurantoin 1.4%. Prevention of ESBL-producing E. coli dissemination, especially for ST131 clade C2, is inevitably necessary for reducing drug resistance and decreasing healthcare-associated infections.

Hospital-Acquired Infections Caused by Carbapenem-Resistant Enterobacteriaceae: An Observational Study

Worldwide, hospital-acquired infections (HAIs) are continuously rising within healthcare settings, leading to high mortality and morbidity rates. Many hospitals have reported the spread of carbapenemases globally, specifically within the E. coli and K. pneumoniae species. This study was aimed at analyzing the state of hospital-acquired, carbapenem-resistant E. coli and K. pneumoniae in the United Kingdom between 2009 and 2021. Moreover, the study analyzed the most efficacious approaches to patient management for controlling the carbapenem-resistant Enterobacteriaceae (CRE) spread. Initially, 1094 articles were identified as relevant for screening, and among them, 49 papers were eligible for full-text screening, with a total of 14 articles meeting the inclusion criteria. The information was recorded from published articles through PubMed, the Web of Science, Scopus, Science Direct, and the Cochrane library and was used to search for hospital-acquired carbapenem-resistant E. coli and K pneumoniae in the UK between 2009 and 2021, in order to evaluate the spread of CRE in hospitals. The total number of carbapenem-resistant E. coli was 1083 and this was 2053 for carbapenem-resistant K. pneumoniae in more than 63 UK hospitals. KPC was the dominant carbapenemase produced by K. pneumoniae. The results showed that the treatment options considered depended on the type of carbapenemase produced; K. pneumoniae showed more resistance to a treatment options, i.e., Colistin, than the other carbapenemase. The current state of the UK is at minimal risk for a CRE outbreak; however, appropriate treatment and infection control measures are highly required to prevent this CRE spread at the regional and global levels. The present study findings have an important message for physicians, healthcare workers, and policymakers about hospital-acquired carbapenem-resistant E. coli and K. pneumoniae spread and approaches to patient management.

Population genomic analysis reveals the emergence of high-risk carbapenem-resistant Escherichia coli among ICU patients in China

OBJECTIVES

The increasing incidence of carbapenem-resistant Enterobacterales (CRE) mediated nosocomial infections has caused a significant public health burden globally. Currently, the prevalence and genomic characteristics of carbapenem-resistant Escherichia coli (CREC) in patients admitted to the intensive care unit (ICU) are unknown.

METHODS

Herein, we present a nationwide genomic investigation of CREC isolates among ICU patients in China in 2018 and 2020. In total, 113 CREC isolates were identified from 1105 samples in 25 hospitals, and investigated with phenotyping and genomics approaches.

RESULTS

Carbapenemases were produced in 94.69% (107/113) of CREC isolates, which comprise KPC-2 (n = 53, 49.53%), NDM (n = 51, 47.66%), IMP-4 (n = 2, 1.87%), and OXA-181 (n = 1, 0.93%). Notably, CREC isolates co-carrying mcr-9 and bla_NDM-5 or tet(X4) and bla_NDM-5 were first identified in clinical settings. The carbapenemase genes of most isolates were located on the plasmids. The bla_KPC gene was mainly mediated by IncFII plasmids (n = 37, 69.81%), and bla_NDM was located on the IncX3 plasmid (n = 36, 70.59%). CREC isolates belonged to diverse sequence types (STs) of which ST131 was the most prevalent bla_KPC-positive CREC isolates (34/113, 30.09%), while bla_NDM was associated with ST617 and ST410 isolates, thereby indicating that multiple CREC clones spread in Chinese ICU patients.

CONCLUSIONS

This study highlights the emerging threat of high-risk CREC isolates such as ST131 circulating in the ICU in China. Hence, stringent monitoring of such high-risk clones should be performed.

Carbapenem-resistant Escherichia coli from shrimp and salmon available for purchase by consumers in Canada: a risk profile using the Codex framework

Resistance to carbapenems in human pathogens is a growing clinical and public health concern. The carbapenems are in an antimicrobial class considered last-resort, they are used to treat human infections caused by multidrug-resistant Enterobacterales, and they are classified by the World Health Organization as 'High Priority Critically Important Antimicrobials'. The presence of carbapenem-resistant Enterobacterales (CREs) of animal-origin is of concern because targeted studies of Canadian retail seafood revealed the presence of carbapenem resistance in a small number of Enterobacterales isolates. To further investigate this issue, a risk profile was developed examining shrimp and salmon, the two most important seafood commodities consumed by Canadians and Escherichia coli, a member of the Enterobacterales order. Carbapenem-resistant E. coli (CREc) isolates have been identified in shrimp and other seafood products. Although carbapenem use in aquaculture has not been reported, several classes of antimicrobials are utilised globally and co-selection of antimicrobial-resistant microorganisms in an aquaculture setting is also of concern. CREs have been identified in retail seafood purchased in Canada and are currently thought to be uncommon. However, data concerning CRE or CREc occurrence and distribution in seafood are limited, and argue for implementation of ongoing or periodic surveillance.

Diversity of carbapenemase-producing Enterobacterales in England as revealed by whole-genome sequencing of isolates referred to a national reference laboratory over a 30-month period

Introduction. Increasing numbers of carbapenemase-producing Enterobacterales (CPE), which can be challenging to treat, have been referred to the national reference laboratory in England since the early 2000s.Gap Statement/Aim. Previous studies on CPE in the UK have focussed on localized outbreaks. We applied whole-genome sequencing (WGS) to isolates referred to the national reference laboratory over 30 months to inform our understanding of CPE epidemiology in England.Methodology. The first confirmed CPE from each new patient referred by an English diagnostic laboratory between 1 January 2014 and 30 June 2016 was sequenced on an Illumina HiSeq 2500. Multiple isolates from the same patient were included from either different species or the same species with different carbapenemase genes. The data were analysed using an in-house bioinformatics pipeline that determines species identification, multi-locus sequence typing (MLST) profile and antimicrobial resistance gene content.Results. A total of 2658 non-duplicate CPE were sequenced amongst which three host organisms belonging to diverse sequence types (STs) predominated: Klebsiella pneumoniae (1380/2658, 51.9 %; 177 STs), Escherichia coli (723/2658, 27.2 %; 133 STs) and Enterobacter cloacae (294/2658, 11.1 %; 88 STs). Thirty different carbapenemase gene variants were identified, although bla _OXA-48-like (1122/2658, 42.2%), bla _NDM (692/2658, 26.0 %), bla _KPC (571/2658, 21.5 %), bla _VIM (100/2658, 3.8 %) and bla _IMP (33/2658, 1.2 %) predominated. ST/carbapenemase gene pairings represented widely distributed high-risk clones or clusters at a regional or hospital level.Conclusion. CPE referred to the national reference laboratory are diverse, suggesting multiple introductions to England and a role for horizontal transfer of carbapenemase genes in English CPE epidemiology.

Meropenem-vaborbactam: a critical positioning for the management of infections by Carbapenem-resistant Enterobacteriaceae

INTRODUCTION

The review aims to review the positioning of meropenem-vaborbactam in clinical practice, taking into consideration the characteristics of other available drugs, namely ceftazidime-avibactam, plazomicin and colistin.

AREAS COVERED

The search terms "meropenem-vaborbactam" or RX7009 for the years 2006 until 2021 were used.

EXPERT OPINION

Coupling of meropenem with the cyclic boronate derivative varobactam enhances considerably the in vitro intrinsic activity of meropenem against isolates producing KPC (Klebsiella pneumoniae-producing carbapenemase). The drug has linear elimination and the ratio of the area under the curve of the free drug to the minimum inhibitory concentration is the main pharmacodynamics variable determining bacterial clearance. Meropenem-vaborbactam is currently approved for the management of complicated urinary tract infections including acute pyelonephritis, complicated intraabdominal infections and hospital-acquired pneumonia including ventilator-associated pneumonia.

Specificities and Commonalities of Carbapenemase-Producing Escherichia coli Isolated in France from 2012 to 2015

Carbapenemase-producing Escherichia coli (CP-Ec) represents a major public health threat with a risk of dissemination in the community as has occurred for lineages producing extended-spectrum β-lactamases. To characterize the extent of CP-Ec spread in France, isolates from screening and infection samples received at the French National Reference Center (F-NRC) laboratory for carbapenemase-producing Enterobacterales were investigated. A total of 691 CP-Ec isolates collected between 2012 and 2015 and 22 isolates collected before 2012 were fully sequenced. Analysis of their genome sequences revealed some disseminating multidrug-resistant (MDR) lineages frequently acquiring diverse carbapenemase genes mainly belonging to clonal complex 23 (CC23) (sequence type 410 [ST410]) and CC10 (ST10 and ST167) and sporadic isolates, including rare ST131 isolates (n = 17). However, the most represented sequence type (ST) was ST38 (n = 92) with four disseminated lineages carrying bla_OXA-48-like genes inserted in the chromosome. Globally, the most frequent carbapenemase gene (n = 457) was bla_OXA-48. It was also less frequently associated with MDR isolates being the only resistance gene in 119 isolates. Thus, outside the ST38 clades, its acquisition was frequently sporadic with no sign of dissemination, reflecting the circulation of the IncL plasmid pOXA-48 in France and its high frequency of conjugation. In contrast, bla_OXA-181 and bla_NDM genes were often associated with the evolution of MDR E. coli lineages characterized by mutations in ftsI and ompC.

IMPORTANCE Carbapenemase-producing Escherichia coli (CP-Ec) might be difficult to detect, as MICs can be very low. However, their absolute number and their proportion among carbapenem-resistant Enterobacterales have been increasing, as reported by WHO and national surveillance programs. This suggests a still largely uncharacterized community spread of these isolates. Here, we have characterized the diversity and evolution of CP-Ec isolated in France before 2016. We show that carbapenemase genes are associated with a wide variety of E. coli genomic backgrounds and a small number of dominant phylogenetic lineages. In a significant proportion of CP-Ec, the most frequent carbapenemase gene bla_OXA-48, was detected in isolates lacking any other resistance gene, reflecting the dissemination of pOXA-48 plasmids, likely in the absence of any antibiotic pressure. In contrast, carbapenemase gene transfer may also occur in multidrug-resistant E. coli, ultimately giving rise to at-risk lineages encoding carbapenemases with a high potential of dissemination.

Whole genome sequencing and characteristics of Escherichia coli with co-existence of ESBL and mcr genes from pigs

This study aimed to analyze three ESBL-producing E. coli co-harboring mcr and ESBL genes from a healthy fattening pig (E. 431) and two sick pigs (ECP.81 and ECP.82) in Thailand using Whole Genome Sequencing (WGS) using either Illumina MiSeq or HiSeq PE150 platforms to determine their genome and transmissible plasmids. E. 431 carrying mcr-2.1 and mcr-3.1 belonged to serotype O142:H31 with ST29 sequence type. ECP.81 and ECP.82 from sick pigs harboring mcr-1.1 and mcr-3.1 were serotype O9:H9 with ST10. Two mcr-1.1 gene cassettes from ECP.81 and ECP.82 were located on IncI2 plasmid with 98% identity to plasmid pHNSHP45. The mcr-2.1-carrying contig in E. 431 showed 100% identity to plasmid pKP37-BE with the upstream flanking sequence of IS1595. All three mcr-3.1-carrying contigs contained the ΔTnAs2-mcr-3.1-dgkA core segment and had high nucleotide similarity (85–100%) to mcr-3.1-carrying plasmid, pWJ1. The mobile elements i.e. IS4321, ΔTnAs2, ISKpn40 and IS3 were identified in the flanking regions of mcr-3. Several genes conferring resistance to aminoglycosides (aac(3)-IIa, aadA1, aadA2b, aph(3’’)-Ib, aph(3’)-IIa and aph(6)-Id), macrolides (mdf(A)), phenicols (cmlA1), sulphonamide (sul3) and tetracycline (tet(A) and tet(M)) were located on plasmids, of which their presence was well corresponded to the host’s resistance phenotype. Amino acid substitutions S83L and D87G in GyrA and S80I and E62K in ParC were observed. The bla_CTX-M-14 and bla_CTX-M-55 genes were identified among these isolates additionally harbored bla_TEM-1B. Co-transfer of mcr-1.1/bla_TEM-1B and mcr-3.1/bla_CTX-M-55 was observed in ECP.81 and ECP.82 but not located on the same plasmid. The results highlighted that application of advanced innovation technology of WGS in AMR monitoring and surveillance provide comprehensive information of AMR genotype that could yield invaluable benefits to development of control and prevention strategic actions plan for AMR.

Molecular Epidemiology and Risk Factors for Extended-Spectrum β-Lactamase-Producing Enterobacterales in Long-Term Care Residents

OBJECTIVES

We aimed to assess the burden of extended-spectrum β-lactamase (ESBL)-producing Enterobacterales in Swiss long-term care facilities (LTCFs) to describe the molecular epidemiology, describe the intrainstitutional and regional clusters of resistant pathogens, and identify independent institution- and resident-level factors associated with colonization.

DESIGN

Cross-sectional study.

SETTING AND PARTICIPANTS

From August to October 2019, we performed a point prevalence study among residents from 16 LTCFs in Western and Eastern Switzerland (8 per region).

METHODS

Residents underwent screening for ESBL-producing Enterobacterales (ESBL-E); whole-genome sequencing (WGS) was performed. We gathered institution-level (eg, number of beds, staff-resident ratio, alcoholic hand rub consumption) and resident-level [eg, anthropometric data, time in facility, dependency, health care exposure, antibiotic treatment, proton-pump inhibitor (PPI) use] characteristics. Factors associated with colonization were identified using a generalized linear model.

RESULTS

Among 1185 eligible residents, 606 (51%) consented to the study. ESBL-E prevalence was 11.6% (70/606), ranging from 1.9% to 33.3% between institutions, with a median of 12.5% in the West and 6.9% in the East (P = .03). Among 59 Escherichia coli (from 58 residents), multilocus sequence type (ST) 131 was most common (n = 43/59, 73%), predominantly its subclone H30R1 (n = 37/43, 86%). WGS data identified multiple intrainstitutional and regional clusters. Independent risk factors for ESBL carriage were previous ESBL colonization [adjusted odds ratio (aOR) 23.5, 95% confidence interval (CI) 6.6-83.8, P < .001), male gender (aOR 2.6, 95% CI 1.5-4.6, P = .002), and use of PPIs (aOR 2.2, 95% CI 1.2-3.8, P = .01).

CONCLUSIONS AND IMPLICATIONS

Overall ESBL-E prevalence in Swiss LTCF residents is low. Yet, we identified several clusters of residents with identical pathogens within the same institution. This implies that particularly affected institutions might benefit from targeted infection control interventions. PPI use was the only modifiable factor associated with carriage of ESBL producers. This study adds to the growing list of adverse outcomes associated with PPIs, calling for action to restrict their use in the long-term care setting.

Global molecular epidemiology of carbapenem-resistant Escherichia coli (2002-2017)

The emergence of carbapenem-resistant (CR) Escherichia coli obliges an assessment of such strains' molecular epidemiology. Accordingly, we characterized in detail a globally distributed collection of CR E. coli isolates, then explored for associations between geographical origin and bacterial traits, and between different bacterial traits. We used established PCR-based assays and broth microdilution MIC determinations to characterize 343 global CR (i.e., non-susceptible to ≥ 1 carbapenem) extraintestinal E. coli isolates (2002-2017) for diverse molecular traits-including phylogroups, sequence types (STs), beta-lactamase genes, and 51 virulence genes-and susceptibility to 12 relevant antimicrobial agents. The study population was tremendously diverse according to all assessed variables. Nonetheless, certain geographically aligned, unifying themes emerged. These included an association of an Asia/West Pacific origin with non-B2/D/F phylogroups and STs, lower molecularly inferred virulence, more extensive resistance, and specific resistance genes (notably, metallo-beta-lactamases). Likewise, U.S. isolates from the central region, vs. other regions, were more virulent-appearing and more often from phylogroup B2 and ST131, but less extensively resistant and more often carbapenemase-gene negative. The global CR E. coli population is highly diverse according to multiple characteristics and varies significantly by geographical region. This predictably will pose challenges for prevention and management, and obliges ongoing surveillance.

Clinical and molecular characteristics of carbapenem non-susceptible Escherichia coli: A nationwide survey from Oman

The prevalence of carbapenem-resistant Enterobacterales (CRE) in the Arabian Peninsula is predicted to be high, as suggested from published case reports. Of particular concern, is carbapenem-resistant E. coli (CR-EC), due to the importance of this species as a community pathogen. Herein, we conducted a comprehensive molecular characterization of putative CR-EC strains from Oman. We aim to establish a baseline for future molecular monitoring. We performed whole-genome sequencing (WGS) for 35 putative CR-EC. Isolates were obtained from patients at multiple centers in 2015. Genetic relatedness was investigated using several typing approaches such as MLST, SNP calling, phylogroup and CRISPR typing. Maxiuium likelihood SNP-tree was performed by RAxML after variant calling and removal of recombination regions with Snippy and Gubbins, respectively. Resistance genes, plasmid replicon types, virulence genes, and prophage were also characterised. The online databases CGE, CRISPRcasFinder, Phaster and EnteroBase were used for the in silico analyses. Screening for mutations in genes regulating the expression of porins and efflux pump as well as mutations lead to fluoroquinolones resistance were performed with CLC Genomics Workbench. The genetic diversity suggests a polyclonal population structure with 21 sequence types (ST), of which ST38 being the most prevalent (11%). SNPs analysis revealed possible transmission episodes. Whereas, CRISPR typing helped to spot outlier strains belonged to phylogroups other than B2 which was CRISPR-free. The virulent phylogroups B2 and D were detected in 4 and 9 isolates, respectively. In some strains bacteriophages acted as vectors for virulence genes. Regarding resistance to β-lactam, 22 were carbapenemase producers, 3 carbapenem non-susceptible but carbapenemase-negative, 9 resistant to expanded-spectrum cephalosporins, and one isolate with susceptibility to cephalosporins and carbapenems. Thirteen out of the 22 (59%) carbapenemase-producing isolates were NDM and 7 (23%) were OXA-48-like which mirrors the situation in Indian subcontinent. Two isolates co-produced NDM and OXA-48-like enzymes. In total, 80% (28/35) were CTX-M-15 producers and 23% (8/35) featured AmpC. The high-risk subclones ST131-H30Rx/C2, ST410-H24RxC and ST1193-H64RxC were detected, the latter associated with NDM. To our knowledge, this is the first report of ST1193-H64Rx subclone with NDM. In conclusion, strains showed polyclonal population structure with OXA-48 and NDM as the only carbapenemases in CR-EC from Oman. We detected the high-risk subclone ST131-H30Rx/C2, ST410-H24RxC and ST1193-H64RxC. The latter was reported with carbapenemase gene for the first time here.

Antimicrobial resistance in ICUs: an update in the light of the COVID-19 pandemic

PURPOSE OF REVIEW

To describe current antimicrobial resistance in ESKAPE Gram-negative microorganisms and their situation in the ICUs, the implication of the so-called high-risk clones (HiRCs) involved in the spread of antimicrobial resistance as well as relevance of the COVID-19 pandemic in the potential increase of resistance.

RECENT FINDINGS

Extended-spectrum and carbapenemase producing Enterobacterales and multidrug and extensive drug-resistant Pseudomonas aeruginosa and Acinetobacter baumannii have increased worldwide. Sequence type (ST)131 Escherichia coli, ST258, ST11, ST10, ST147 and ST307 Klebsiella pneumoniae, ST111, ST175, ST235 and ST244 P. aeruginosa HiRCs are responsible for this increase in the ICUs, and some of them are implicated in the emergence of resistance mechanisms affecting new antimicrobials. A similar situation can be found with European clonal complex 1 and clonal complex 2 of A. baumannii. The high use of antimicrobials during the COVID-19 pandemic, particularly in ICUs, might have a negative influence in future trends of antimicrobial resistance.

SUMMARY

The increase of antimicrobial resistance in ICUs is mainly due to the spread of HiRCs and is exemplified with the ESKAPE Gram-negative microorganisms. The COVID-19 pandemic might have a negative impact in the increase of antimicrobial resistance and should be monitored through specific surveillance studies in ICUs.

Whole genome sequence of an Escherichia coli ST131 strain isolated from a patient with bloodstream infection in China co-harbouring blaKPC-2, blaCTX-M-3, blaCTX-M-14, qnrS1, aac(3)-IIa and aac(6')-Ib-cr genes

OBJECTIVES

Escherichia coli sequence type 131 (ST131) is an international multiresistant high-risk clone associated with a large number of clinical infections. Here we report the draft genome sequence of a ST131 clinical isolate (EC538) obtained from a patient with bloodstream infection (BSI) in China co-harbouring the bla_KPC-2, bla_CTX-M-3, bla_CTX-M-14, qnrS1, aac(3)-IIa and aac(6')-Ib-cr genes.

METHODS

Antimicrobial susceptibility testing of E. coli EC538 was performed. DNA of E. coli EC538 was extracted and was sequenced using an Illumina HiSeq^TM X Ten platform. Generated sequence reads were assembled using CLC Genomics Workbench. Contigs were annotated using Rapid Annotation using Subsystem Technology (RAST), and further bioinformatics analyses were performed.

RESULTS

The total number of assembled bases was 5 420 040bp, with 5611 protein-coding sequences. Escherichia coli EC538 belongs to ST131 by multilocus sequence typing (MLST). The presence of bla_KPC-2, bla_CTX-M-3 and bla_CTX-M-14 genes was detected in addition to other antimicrobial resistance genes conferring resistance to fluoroquinolones, aminoglycosides, trimethoprim, sulfonamides, tetracyclines, macrolides and rifampicin.

CONCLUSION

To our knowledge, this is the first report of an E. coli ST131 strain from a BSI co-harbouring bla_KPC-2, bla_CTX-M-3, bla_CTX-M-14, qnrS1, aac(3)-IIa and aac(6')-Ib-cr genes in China. The presented genome sequence of a carbapenemase-producing E. coli ST131 strain could provide further insight into the genomic diversity of this highly virulent, multiresistant and successfully pandemic bacterial pathogen.

Whole Genome Sequencing and Characteristics of mcr-1-Harboring Plasmids of Porcine Escherichia coli Isolates Belonging to the High-Risk Clone O25b:H4-ST131 Clade B

Porcine Escherichia coli ST131 isolates are scarcely documented. Here, whole genome sequencing and core genome (CG) and plasmidome analysis of seven isolates collected from diarrheic piglets and four from pork meat were performed. All of the 11 ST131 isolates belonged to serotype O25b:H4 and clade B and showed fimH22 allele or mutational derivatives. The 11 porcine isolates possessed virulence traits that classified the isolates as avian pathogenic, uropathogenic, and extraintestinal pathogenic E. coli–like (APEC-, UPEC-, and ExPEC-like) and constituted virotype D. The CG was performed for all porcine isolates in addition to 73 ST131 reference isolates from different origins. Within clade B, the CG showed nine subclusters, allowing us to describe five new subclades (B6, B6-like, B7, B8, and B9). There was an association between subclade B6, PST43, virotype D2, and food origin, whereas subclade B7 included PST9 isolates with virotype D5 from diarrheic piglets (p = 0.007). The distance between human and porcine isolates from subclades B6 and B7 had an average of 20 and 15 SNP/Mb, respectively. [F2:A-:B1]-IncF, ColE1-like, and IncX plasmids were the most prevalent. Besides, IncF plasmids harbored a ColV region frequent among APEC isolates. Antimicrobial resistance genes conferring resistance to penicillin, tetracycline, quinolones, and colistin were the most common. The mcr-1.1 gene was detected in 5 of 11 porcine isolates, integrated into the chromosome of one isolate and into plasmids in the remainder isolates (two MOB_H11/IncHI2-ST4, one MOB_P3/IncX4, and one MOB_F12/IncF [F2:A-:B1] supposedly cointegrated with an IncHI2). The surrounding environments of the mcr-1 cassette showed variability. However, there were conserved structures within the same plasmid family. In conclusion, CG analysis defined five new subclades. The ST131 porcine isolates belonged to new subclades B6 and B7. Moreover, porcine and clinical human isolates were strongly related. The 11 porcine ST131 isolates harbored a wide variety of plasmids, virulence, and resistance genes. Furthermore, epidemic plasmids IncX4 and IncHI2 are responsible for the acquisition of mcr-1.1 gene. We hypothesize that the APEC-IncF plasmid acquired the mcr-1.1 gene via cointegrating an IncHI2 plasmid, which is worrying due to combination of virulence and resistance attributes in a single mobile genetic element.