Potential spread of mcr-9-carrying IncHI2 plasmids in Enterobacter hormaechei in Vietnam

Integrated analysis of patient networks and plasmid genomes reveals a regional, multi-species outbreak of carbapenemase-producing Enterobacterales carrying both blaIMP and mcr-9 genes

BACKGROUND

Carbapenemase-producing Enterobacterales (CPE) are challenging in healthcare, with resistance to multiple classes of antibiotics. This study describes the emergence of IMP-encoding CPE amongst diverse Enterobacterales species between 2016 and 2019 across a London regional network.

METHODS

We performed a network analysis of patient pathways, using electronic health records, to identify contacts between IMP-encoding CPE positive patients. Genomes of IMP-encoding CPE isolates were overlayed with patient contacts to imply potential transmission events.

RESULTS

Genomic analysis of 84 Enterobacterales isolates revealed diverse species (predominantly Klebsiella spp, Enterobacter spp, E. coli); 86% (72/84) harboured an IncHI2 plasmid carrying blaIMP and colistin resistance gene mcr-9 (68/72). Phylogenetic analysis of IncHI2 plasmids identified three lineages showing significant association with patient contacts and movements between four hospital sites and across medical specialities, which was missed on initial investigations.

CONCLUSIONS

Combined, our patient network and plasmid analyses demonstrate an interspecies, plasmid-mediated outbreak of blaIMPCPE, which remained unidentified during standard investigations. With DNA sequencing and multi-modal data incorporation, the outbreak investigation approach proposed here provides a framework for real-time identification of key factors causing pathogen spread. Plasmid-level outbreak analysis reveals that resistance spread may be wider than suspected, allowing more interventions to stop transmission within hospital networks.

Emergence of OXA-48-producing Enterobacter hormaechei in a Swiss companion animal clinic and their genetic relationship to clinical human isolates

BACKGROUND

Enterobacter hormaechei producing the carbapenemase OXA-48 was identified repeatedly in infections in companion animals hospitalized at a Swiss veterinary clinic where OXA-48-producing Klebsiella pneumoniae was previously reported.

OBJECTIVES

To determine the genetic relatedness of animal and human E. hormaechei strains collected in Switzerland during 2017-22 and their mobile genetic elements.

METHODS

Hybrid assemblies for phylogenetic and comparative analysis of animal (n = 9) and human (n = 25) isolates were obtained by sequencing with Illumina, PacBio and Oxford Nanopore Technologies. Antimicrobial susceptibility was tested by broth microdilution.

RESULTS

The animal strains were identified as E. hormaechei subsp. xiangfangensis ST114 (n = 6) and ST418 (n = 2), and E. hormaechei subsp. hoffmannii ST78 (n = 1). Human E. hormaechei belonged to subspecies steigerwaltii (n = 10), xiangfangensis (n = 13), hoffmannii (n = 1) and hormaechei (n = 1), with a heterogeneous ST distribution differing from the animal strains, except for two ST114. Core-gene SNP analysis confirmed the clonality of the animal ST114 and ST418 isolates (0 to 10 SNPs), and close relatedness of animal and human ST114 strains (80-120 SNPs). The strains harboured the blaOXA-48 gene on ca. 63 kb IncL-type plasmids (n = 27); on ca. 72 kb IncL plasmids co-harbouring blaCTX-M-14 (n = 2); and on ca. 150-180 kb IncFIB (n = 4) or hybrid IncFIB/IncL (n = 1) plasmids. The blaOXA-48-harbouring plasmids and the blaDHA-1-carrying ISCR1 element in one animal ST114 and both ST418 clones were likely acquired from previously spreading K. pneumoniae strains.

CONCLUSIONS

Common ecological niches favour the spread of plasmid-borne carbapenemases among Enterobacterales and the emergence of MDR E. hormaechei clones.

Multidrug-resistant isolates from Ukrainian patients in a German health facility: a genomic surveillance study focusing on antimicrobial resistance and bacterial relatedness

PURPOSE

Antimicrobial resistance is a pressing issue in Ukraine, with healthcare-associated infections caused by multidrug-resistant organisms being a major concern. A recent prospective multicenter study revealed a staggering rate of 48.4% antimicrobial resistance to carbapenems among Enterobacterales causing a healthcare-associated infection. We conducted a systematic survey to investigate the incidence rate and incidence density of carbapenemase-producing Gram-negative bacteria (CPGN) among refugees and war-wounded Ukrainians in connection with the German health system.

METHODS

From the onset of the war until November 2022, seven Ukrainian patients were admitted to our hospital. Upon admission, screening samples and samples from the focus of suspected infection were taken from all seven patients. The incidence rate and the incidence density of CPGN were calculated as a result of the microbiological findings. We sequenced all CPGN using Illumina technology.

RESULTS

The incidence rate of CPGN at our hospital was 0.06 for 2021 and 0.18 for 2022. All seven Ukrainian patients were infected or colonized with at least one CPGN, including K. pneumoniae (14/25), P. aeruginosa (6/25), A. baumannii (1/25), Providencia stutartii (1/25), C. freundii (1/25), and E. coli (2/25). Genomic surveillance revealed that (i) most frequently detected carbapenemases among all sequenced isolates were blaNDM (17/25) and blaOXA-48 (6/25), (ii) most commonly observed plasmid replicons among the K. pneumoniae isolates recovered from Ukrainian patients were Col(pHAD28) (12/14), IncHI1B(pNDM-MAR) (9/14), IncFIB(pNDM-Mar) (12/14), and (iii) clonal relation between the pathogens of the Ukrainian isolates, but not for the isolates from our hospital surveillance system.

CONCLUSION

The rising prevalence of community-acquired colonization and infection with CPGN is having a direct effect on the infection prevention measures, such as higher number of isolations, reprocessing of patient rooms, additional microbiological testing and overall organization within hospitals.

Situation Report on mcr-Carrying Colistin-Resistant Clones of Enterobacterales: A Global Update Through Human-Animal-Environment Interfaces

In the twenty-first century, antibiotic resistance (ABR) is one of the acute medical emergencies around the globe, overwhelming human-animal-environmental interfaces. Hit-or-mis use of antibiotics exacerbates the crisis of ABR, dispersing transferable resistance traits and challenging treatment regimens based on life-saving drugs such as colistin. Colistin is the highest priority critically important antimicrobials for human medicine, but its long use as a growth promoter in animal husbandry reduces clinical efficacy. Since 2015, the emergence and spread of mobile colistin resistance (mcr)-carrying colistin-resistant clones of Enterobacterales have been markedly sustained in both humans and animals, especially in developing countries. Hospital and community transmissions of mcr clones pose a high risk for infection prevention and outbreaks at the national and international levels. Several public health and limited one health studies have highlighted the genomic insights of mcr clones, clarifying the chromosomal sequence types (STs) and plasmid incompatibility (Inc) types. But this information is segregated into humans and animals, and rarely are environmental sectors complicating the understanding of possibly intercontinental and sectoral transmission of these clones. India is the hotspot for superbugs, including mcr-carrying colistin-resistant isolates that threaten cross-border transmission. The current review provided an up-to-date worldwide scenario of mcr-carrying STs and plasmid Inc types among the Gram-negative bacilli of Enterobacterales across human-animal-environmental interfaces and correlated with the available information from India.

Emergence of carbapenem-resistant Enterobacter hormaechei ST93 plasmids co-harbouring blaNDM-1, blaKPC-2, and mcr-9 in bloodstream infection

OBJECTIVES

We isolated a strain of Enterobacter hormaechei, ECC2783, co-harbouring blaNDM-1, blaKPC-2 and mcr-9 plasmids from a bloodstream infection and investigated its biological features.

METHODS

The presence of carbapenemase genes and mcr-9 was confirmed by polymerase chain reaction amplification. Whole genome sequencing and genomic analysis were performed on ECC2783. Experiments assessing the conjugation and stability of plasmids carrying the carbapenemase gene were performed. We also performed a colistin resistance induction experiment and studied the fitness cost of transconjugants.

RESULTS

ECC2783 has an extensive drug resistance phenotype. Multilocus sequence typing analysis results showed that ECC2783 belongs to sequence type 93. Bioinformatics analysis confirmed that ECC2783 has four plasmids, of which pECC2783_a, carrying mcr-9, is the IncHI2 type, and pECC2783_c, carrying blaNDM-1, is the IncX3 type. pECC2783_d, carrying blaKPC-2, is an unclassified type. We successfully obtained two transconjugants (J53/ECC2783_1, carrying blaNDM-1, and J53/ECC2783_2, carrying blaKPC-2 and blaNDM-1). There was no statistically significant difference in the relative growth rate between J53 and J53/ECC2783_2.

CONCLUSION

For the first time, we isolated carbapenem-resistant E. hormaechei plasmids co-harbouring blaNDM-1, blaKPC-2, and mcr-9 from a patient with a blood stream infection. This isolate has a survival advantage in a hospital environment, and its clinical monitoring should be strengthened.

First reported detection of the mobile colistin resistance genes, mcr-8 and mcr-9, in the Irish environment

The emergence and dissemination of mobile colistin resistance (mcr) genes across the globe poses a significant threat to public health, as colistin remains one of the last line treatment options for multi-drug resistant infections. Environmental samples (157 water and 157 wastewater) were collected in Ireland between 2018 and 2020. Samples collected were assessed for the presence of antimicrobial resistant bacteria using Brilliance ESBL, Brilliance CRE, mSuperCARBA and McConkey agar containing a ciprofloxacin disc. All water and integrated constructed wetland influent and effluent samples were filtered and enriched in buffered peptone water prior to culture, while wastewater samples were cultured directly. Isolates collected were identified via MALDI-TOF, were tested for susceptibility to 16 antimicrobials, including colistin, and subsequently underwent whole genome sequencing. Overall, eight mcr positive Enterobacterales (one mcr-8 and seven mcr-9) were recovered from six samples (freshwater (n = 2), healthcare facility wastewater (n = 2), wastewater treatment plant influent (n = 1) and integrated constructed wetland influent (piggery farm waste) (n = 1)). While the mcr-8 positive K. pneumoniae displayed resistance to colistin, all seven mcr-9 harbouring Enterobacterales remained susceptible. All isolates demonstrated multi-drug resistance and through whole genome sequencing analysis, were found to harbour a wide variety of antimicrobial resistance genes i.e., 30 ± 4.1 (10-61), including the carbapenemases, bla_OXA-48 (n = 2) and bla_NDM-1 (n = 1), which were harboured by three of the isolates. The mcr genes were located on IncHI2, IncFIIK and IncI1-like plasmids. The findings of this study highlight potential sources and reservoirs of mcr genes in the environment and illustrate the need for further research to gain a better understanding of the role the environment plays in the persistence and dissemination of antimicrobial resistance.

Distribution and Antibiotic Resistance Characteristics of Bacteria Isolated from Blood Culture in a Teaching Hospital in Vietnam During 2014-2021

Purpose

Studies on the epidemiology of bloodstream infection (BSI) and antimicrobial resistance (AMR) are limited in Vietnam. Thus, the present study aimed to elucidate the epidemiology of BSI and AMR of BSI-causing bacteria in Vietnam.

Methods

Data regarding blood cultures from 2014 to 2021 were collected and analyzed using the chi-square test, Cochran-Armitage test, and binomial logistic regression model.

Results

Overall, 2405 (14.15%) blood cultures were positive during the study period. In total, 55.76% of BSIs occurred in patients aged ≥60 years. The male-to-female ratio of patients with BSI was 1.87:1. Escherichia coli (26.11%), Staphylococcus aureus (15.79%), Klebsiella pneumoniae (10.44%), Acinetobacter baumannii (4.70%), and Pseudomonas aeruginosa (3.45%) were the leading bacterial species causing BSI. The AMR rate of these bacteria isolated in the intensive care unit (ICU) was significantly higher compared with that of those in other wards. E. coli was the least resistant to carbapenems (2.39%-4.14%), amikacin (3.85%), and colistin (11.54%) and most resistant to penicillins (>80.0%). S. aureus was the least resistant to glycopeptides (0%-3.38%), quinupristin-dalfopristin (0.59%), and linezolid (1.02%) and most resistant to clindamycin (71.57%). K. pneumoniae was the least resistant to ertapenem (8.86%), amikacin (9.39%), and colistin (15.38%) and most resistant to aztreonam (83.33%). A. baumannii was the least resistant to amikacin (16.67%) and colistin (16.67%) and highly resistant to other antibiotics (≥50.0%). P. aeruginosa was the least resistant to colistin (16.33%) and piperacillin (28.17%) and highly resistant to other antibiotics (≥50.0%). Notably, the multidrug resistance rate of E. coli (76.41%) was the highest among common pathogens, followed by A. baumannii (71.57%), P. aeruginosa (64.56%), S. aureus (56.99%), and K. pneumoniae (43.72%).

Conclusion

The AMR rate of BSI-causing bacteria, particularly strains isolated from ICU, was alarmingly high. There is a need for new antibiotics, therapeutic strategies, as well as prevention and control to combat BSI and AMR.

Epidemiology and Traits of Mobile Colistin Resistance (mcr) Gene-Bearing Organisms from Horses

Mobile colistin resistance (mcr) genes (mcr-1 to mcr-10) threaten the efficacy of colistin (COL), a polymyxin antibiotic that is used as a last-line agent for the treatment of deadly infections caused by multidrug-resistant and extensively drug-resistant bacteria in humans and animals. COL has been used for more than 60 years for the prophylactic control and treatment of infections in livestock husbandry but not in horses. Polymyxin B is used for the prophylactic control and empirical treatment of infections in horses without conducting sensitivity tests. The lack of sensitivity testing exerts selection pressure for the acquisition of the mcr gene. By horizontal transfer, mcr-1, mcr-5, and mcr-9 have disseminated among horse populations globally and are harbored by Escherichia coli, Klebsiella, Enterobacter, Citrobacter, and Salmonella species. Conjugative plasmids, insertion sequences, and transposons are the backbone of mcr genes in the isolates, which co-express genes conferring multi- to extensive-drug resistance, including genes encoding extended-spectrum β-lactamase, ampicillinase C, fosfomycin, and fluoroquinolone resistance, and virulence genes. The transmission of mcr genes to/among bacterial strains of equine origin is non-clonal. Contact with horses, horse manure, feed/drinking water, farmers, farmers’ clothing/farm equipment, the consumption of contaminated horse meat and its associated products, and the trading of horses, horse meat, and their associated products are routes for the transmission of mcr-gene-bearing bacteria in, to, and from the equine industry.

Emergence of Neonatal Sepsis Caused by MCR-9- and NDM-1-Co-Producing Enterobacter hormaechei in China

Mobile colistin resistance (mcr) genes represent an emerging threat to public health. Reports on the prevalence, antimicrobial profiles, and clonality of MCR-9-producing Enterobacter cloacae complex (ECC) isolates on a national scale in China are limited. We screened 3,373 samples from humans, animals, and the environment and identified eleven MCR-9-positive ECC isolates. We further investigated their susceptibility, epidemiology, plasmid profiles, genetic features, and virulence potential. Ten strains were isolated from severe bloodstream infection cases, especially three of them were recovered from neonatal sepsis. Enterobacter hormaechei was the most predominant species among the MCR-9-producing ECC population. Moreover, the co-existence of MCR-9, CTX-M, and SHV-12 encoding genes in MCR-9-positive isolates was globally observed. Notably, mcr-9 was mainly carried by IncHI2 plasmids, and we found a novel ~187 kb IncFII plasmid harboring mcr-9, with low similarity with known plasmids. In summary, our study presented genomic insights into genetic characteristics of MCR-9-producing ECC isolates retrieved from human, animal, and environment samples with one health perspective. This study is the first to reveal NDM-1- and MCR-9-co-producing ECC from neonatal sepsis in China. Our data highlights the risk for the hidden spread of the mcr-9 colistin resistance gene.