IncH-type plasmid harboring bla CTX-M-15, bla DHA-1, and qnrB4 genes recovered from animal isolates

Whole genome sequence analysis of ESBL-producing Escherichia coli recovered from New Zealand freshwater sites

Extended-spectrum beta lactamase (ESBL)-producing Escherichia coli are often isolated from humans with urinary tract infections and may display a multidrug-resistant phenotype. These pathogens represent a target for a One Health surveillance approach to investigate transmission between humans, animals and the environment. This study examines the multidrug-resistant phenotype and whole genome sequence data of four ESBL-producing E. coli isolated from freshwater in New Zealand. All four isolates were obtained from a catchment with a mixed urban and pastoral farming land-use. Three isolates were sequence type (ST) 131 (CTX-M-27-positive) and the other ST69 (CTX-M-15-positive); a phylogenetic comparison with other locally isolated strains demonstrated a close relationship with New Zealand clinical isolates. Genes associated with resistance to antifolates, tetracyclines, aminoglycosides and macrolides were identified in all four isolates, together with fluoroquinolone resistance in two isolates. The ST69 isolate harboured the bla _CTX-M-15 gene on a IncHI2A plasmid, and two of the three ST131 isolates harboured the bla _CTX-M-27 genes on IncF plasmids. The last ST131 isolate harboured bla _CTX-M-27 on the chromosome in a unique site between gspC and gspD. These data highlight a probable human origin of the isolates with subsequent transmission from urban centres through wastewater to the wider environment.

Characterization of qnrB-carrying plasmids from ESBL- and non-ESBL-producing Escherichia coli

BACKGROUND

Escherichia coli carrying clinically important antimicrobial resistances [i.e., against extended-spectrum-beta-lactamases (ESBL)] are of high concern for human health and are increasingly detected worldwide. Worryingly, they are often identified as multidrug-resistant (MDR) isolates, frequently including resistances against quinolones/fluoroquinolones.

RESULTS

Here, the occurrence and genetic basis of the fluoroquinolone resistance enhancing determinant qnrB in ESBL-/non-ESBL-producing E. coli was investigated. Overall, 33 qnrB-carrying isolates out of the annual German antimicrobial resistance (AMR) monitoring on commensal E. coli (incl. ESBL-/AmpC-producing E. coli) recovered from food and livestock between 2013 and 2018 were analysed in detail. Whole-genome sequencing, bioinformatics analyses and transferability evaluation was conducted to characterise the prevailing qnrB-associated plasmids. Furthermore, predominant qnrB-carrying plasmid-types were subjected to in silico genome reconstruction analysis. In general, the qnrB-carrying E. coli were found to be highly heterogenic in their multilocus sequence types (STs) and their phenotypic resistance profiles. Most of them appeared to be MDR and exhibited resistances against up to ten antimicrobials of different classes. With respect to qnrB-carrying plasmids, we found qnrB19 located on small Col440I plasmids to be most widespread among ESBL-producing E. coli from German livestock and food. This Col440I plasmid-type was found to be highly conserved by exhibiting qnrB19, a pspF operon and different genes of unassigned function. Furthermore, we detected plasmids of the incompatibility groups IncN and IncH as carriers of qnrB. All qnrB-carrying plasmids also exhibited virulence factors and various insertion sequences (IS). The majority of the qnrB-carrying plasmids were determined to be self-transmissible, indicating their possible contribution to the spread of resistances against (fluoro)quinolones and other antimicrobials.

CONCLUSION

In this study, a diversity of different plasmid types carrying qnrB alone or in combination with other resistance determinants (i.e., beta-lactamase genes) were found. The spread of these plasmids, especially those carrying antimicrobial resistance genes against highest priority critically important antimicrobial agents, is highly unfavourable and can pose a threat for public health. Therefore, the dissemination pathways and evolution of these plasmids need to be further monitored.

Formation, Transmission, and Dynamic Evolution of a Multidrug-Resistant Chromosomally Integrated Plasmid in Salmonella Spp

IncHI2 plasmids, possessing high flexibility and genetic plasticity, play a vital role in the acquisition and transmission of resistance determinants. Polymorphic mobile genetic elements (MGEs) generated by a chromosomally integrated IncHI2 plasmid in an individual Salmonella isolate have not yet been detected, and the mechanisms of the formation, excision, and dynamic evolution of a multidrug-resistant chromosomally integrated plasmid (MRCP) have remained obscure. Herein, we identified a 260-kb bla_CTX–M–55-qnrS1-bearing IncHI2 plasmid within a Salmonella Muenster strain. Plenty of heterogeneous MGEs (new Escherichia coli chromosomally integrated plasmid or circular plasmids with different profiles) were yielded when this MRCP was conjugated into E. coli J53 with a transfer frequency of 10^–4–10^–5 transconjugants per donor. A bioinformatic analysis indicated that replicative transposition and homologous recombination of IS26 elements were particularly active, and the truncated Tn1721 also played a vital role in the formation of MRCP offspring. More importantly, when released from the chromosome, MRCP could capture and co-transfer adjacent chromosomal segments to form larger plasmid progeny than itself. Stability and growth kinetics assays showed that the biological characteristics of MRCP progeny were differentiated. This study provides an insight into a flexible existence of MRCP. The conversion between vertical and horizontal transmission endowed MRCP with genetic stability as a chromosomal coding structure and transferability as extra-chromosomal elements. This alternation may accelerate the acquisition and persistence of antibiotic resistance of clinical pathogens and enhance their ability to respond to adverse environments, which poses a great challenge to the traditional antibiotic treatment.

Presence of NDM in non-E. coli Enterobacteriaceae in the poultry production environment

OBJECTIVES

Characterization of non-Escherichia coli NDM-carrying Enterobacteriaceae in the poultry production environment.

METHODS

A total of 36 NDM-positive Enterobacteriaceae (22 Klebsiella pneumoniae, 13 Enterobacter cloacae and 1 Salmonella enterica) were isolated from a chicken farm and WGS was conducted using Illumina Hiseq2500. The genomic characterization of the isolates acquired through WGS analysis included the genomic context-flanking blaNDM genes, MLST, the antibiotic resistance genes (ARGs) and replicon types of plasmids. WGS information for another 73 K. pneumoniae isolates from different sources was retrieved from GenBank and then combined with isolates in this study for comparative genomic and phylogenetic analysis.

RESULTS

Three types of genetic environment carrying blaNDM were identified in 36 non-E. coli Enterobacteriaceae isolates. Sequence comparison analysis indicated these genetic environments were completely identical to our previous findings. WGS further revealed three major types of plasmids (IncFIB, IncX3 and IncFII) from these isolates and the phylogenetic analysis suggested several K. pneumoniae isolates with ST11, ST37 and ST147 from the commercial chicken farm that were closely related to isolates of human origin.

CONCLUSIONS

The blaNDM-harbouring genetic contexts were identified not only in E. coli, but also in K. pneumoniae, E. cloacae and S. enterica, which may indicate that blaNDM has been widely disseminated to non-E. coli Enterobacteriaceae species in animal farms. The close relationship of K. pneumoniae isolates from different origins suggests they could serve as a key vehicle for the transfer of ARGs between humans and food animal production environments.

First Clinical Case of In Vivo Acquisition of DHA-1 Plasmid-Mediated AmpC in a Salmonella enterica subsp. enterica Isolate

A pan-susceptible Salmonella enterica serovar Worthington isolate was detected in the stool of a man returning from Sri Lanka. Under ceftriaxone treatment, a third-generation cephalosporin (3GC)-resistant Salmonella Worthington was isolated after 8 days. Molecular analyses indicated that the two isolates were identical. However, the latter strain acquired a blaDHA-1-carrying IncFII plasmid probably from a Citrobacter amalonaticus isolate colonizing the gut. This is the first report of in vivo acquisition of plasmid-mediated resistance to 3GCs in S. enterica.

Transferable Mechanisms of Quinolone Resistance from 1998 Onward

While the description of resistance to quinolones is almost as old as these antimicrobial agents themselves, transferable mechanisms of quinolone resistance (TMQR) remained absent from the scenario for more than 36 years, appearing first as sporadic events and afterward as epidemics. In 1998, the first TMQR was soundly described, that is, QnrA. The presence of QnrA was almost anecdotal for years, but in the middle of the first decade of the 21st century, there was an explosion of TMQR descriptions, which definitively changed the epidemiology of quinolone resistance. Currently, 3 different clinically relevant mechanisms of quinolone resistance are encoded within mobile elements: (i) target protection, which is mediated by 7 different families of Qnr (QnrA, QnrB, QnrC, QnrD, QnrE, QnrS, and QnrVC), which overall account for more than 100 recognized alleles; (ii) antibiotic efflux, which is mediated by 2 main transferable efflux pumps (QepA and OqxAB), which together account for more than 30 alleles, and a series of other efflux pumps (e.g., QacBIII), which at present have been sporadically described; and (iii) antibiotic modification, which is mediated by the enzymes AAC(6')Ib-cr, from which different alleles have been claimed, as well as CrpP, a newly described phosphorylase.

The CRISPR-Cas system in Enterobacteriaceae

In nature, microorganisms are constantly exposed to multiple viral infections and thus have developed many strategies to survive phage attack and invasion by foreign DNA. One of such strategies is the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated proteins (Cas) bacterial immunological system. This defense mechanism is widespread in prokaryotes including several families such as Enterobacteriaceae. Much knowledge about the CRISPR-Cas system has been generated, including its biological functions, transcriptional regulation, distribution, utility as a molecular marker and as a tool for specific genome editing. This review focuses on these aspects and describes the state of the art of the CRISPR-Cas system in the Enterobacteriaceae bacterial family.

Diverse Plasmids Harboring blaCTX-M-15 in Klebsiella pneumoniae ST11 Isolates from Several Asian Countries

To reveal whether an increase of CTX-M-15-producing Klebsiella pneumoniae ST11 isolates is due to clonal dissemination across the countries, plasmids (pHK02-026, pM16-13, pIN03-01, and pTH02-34) were extracted from four K. pneumoniae isolates collected in Hong Kong, Malaysia, Thailand, and Indonesia, respectively. Complete sequencing of bla_CTX-M-15-carrying plasmids was performed. In addition to the four plasmids, a previously sequenced plasmid (pKP12226) of a K. pneumoniae ST11 isolate from Korea was included in the analysis. While pIN03-01 and pTH02-34, which belonged to the incompatibility group IncX3, showed nearly the same structure, the others of IncF1A or IncFII exhibited very different structures. The number and kinds of antibiotic genes found in the plasmids were also different from each other. Cryptic prophage genes were identified in all five bla_CTX-M-15-harboring plasmids from the ST11 isolates; P1-like region in pKP12226, CPZ-55 prophage region in pHK02-026, phage shock operon pspFABCD in pM16-13, and SPBc2 prophage yokD in pIN03-01 and pTH02-34. The plasmids with bla_CTX-M-15 in the prevailing K. pneumoniae ST11 isolates in Asian countries might emerge from diverse origins by recombination. The prevalence of CTX-M-15-producing K. pneumoniae ST11 clone in Asian countries is not mainly due to the dissemination of a single strain.

Characterization of the population structure, drug resistance mechanisms and plasmids of the community-associated Enterobacter cloacae complex in China

Objectives

To investigate the population structure, drug resistance mechanisms and plasmids of community-associated Enterobacter cloacae complex (CA-ECC) isolates in China.

Methods

Sixty-two CA-ECC isolates collected from 31 hospitals across China were typed by hsp60 typing and MLST. ESBL and AmpC-overexpression phenotype was determined by double-disc synergy test. Replicon typing and conjugation were performed for plasmid analysis. All ESBL-positive isolates and representative conjugants were subjected to detailed characterization by WGS.

Results

Enterobacter hormaechei and Enterobacter kobei were predominant in our collections. MLST distinguished 46 STs with a polyclonal structure. ST591 was the most prevalent clone detected in northern China. Twenty-two isolates (35.5%) were ESBL positive and half of them were E. kobei. ESBL positivity was related to ESBL production (15/22) and to AmpC overexpression (18/22). Core-genome phylogenetic analysis identified intra- and inter-regional dissemination of ESBL-producing E. kobei clones. ESBL producers were exclusively classified as E. hormaechei and E. kobei, and blaCTX-M-3 was the most prevalent ESBL genotype (10/15) detected in four different environments. In the ESBL-positive population, the ESBL producers encoded more drug resistance genes (8-24 genes) by carrying more plasmids (1-3 plasmids) than the non-ESBL-producing isolates, resulting in an inter-group difference in drug susceptibilities. IncHI-type plasmids were prevalent in the ESBL producers (12/15). All IncHI2-type plasmids (n = 11) carried ESBL genes and shared a similar backbone to p09-036813-1A_261 recovered from Salmonella enterica in Canada.

Conclusions

The species-specific distribution, species-dependent ESBL mechanism and endemic plasmids identified in our study highlight the necessity for tailored surveillance of CA-ECC in the future.

Plasmids carrying DHA-1 β-lactamases

The aim of this review is to provide an update on the plasmids mediating DHA-1 cephalosporinase in Klebsiella pneumoniae. These plasmids have been mainly found in this bacterium but not only. The first was isolated from Salmonella sp. in France in the early 1990s. They are currently reported worldwide. Bla_DHA-1 beta-lactamase gene is usually co-expressed with many other antibiotic resistance genes such as extended-spectrum β-lactamases (bla_CTX-M-, bla _SHV -types), oxacillinases (bla_OXA-1, bla_OXA-30), penicillinases (bla _TEM -type), carbapenemases (bla _OXA48 , bla_KPC-2), aminoglycosides (aacA, aadA, armA), fluoroquinolones (qnrB4, aac6'-1b-cr), and sulfonamide (sul1) resistance genes. Plasmids carrying DHA-1 cephalosporinase have different sizes (22 to 313 kb), belong to diverse groups of incompatibility (R, L/M, FII(k), FIB, A/C2, HI2, HIB), and are self-transferable or not. The multidrug resistance region consists of a mosaic structure composed of resistance genes, insertion sequences, composite transposon, and integrons.

Endemic Indian clones of Klebsiella pneumoniae-harbouring New Delhi metallo-beta-lactamase-1 on a hybrid plasmid replicon type: A case of changing New Delhi metallo-beta-lactamase plasmid landscapes in India?

PURPOSE

blaNDM genes are MBL genes that confer resistance to carbapenems. Globally, they are associated with diverse clones and plasmids. In this study, we characterised three isolates of Klebsiella pneumoniae-harbouring blaNDM1 from patients undergoing chronic haemodialysis and renal transplantation.

MATERIALS AND METHODS

3 blaNDM1 -producing K. pneumoniae were isolated from end-stage renal disease patients undergoing haemodialysis and renal transplantation from a nephrology unit. All the three isolates were screened for clinically relevant resistant genes. Plasmid replicon content was analysed by polymerase chain reaction based replicon typing. Conjugation assays were done using azide-resistant Escherichia coli J53 as the recipient strain. Multilocus sequence typing and variable number tandem repeat typing were done to find the clonality. Replicon sequence based typing was attempted to find the diversity of replicon-associated sequences in IncHI3 plasmids.

RESULTS

All the 3 blaNDM positive isolates possessed the New Delhi metallo-beta-lactamase-1 (NDM-1) allele with an IncHI3 plasmid which was not transferable in one isolate. The isolates were found to be sequence type 14 (ST14; 2 nos) and ST38 both of which were previously reported to be the NDM-producing K. pneumoniae STs prevalent in India. Replicon sequence analysis revealed limited sequence diversity within the repHI3 and repFIB locus.

CONCLUSION

To the best of our knowledge, this is the first report of IncHI3, a newly assigned enterobacterial plasmid incompatibility group from India. This could either be a case of importation or a widely circulating NDM plasmid type in India.

Finished Genome Sequence of the Highly Multidrug-Resistant Human Urine Isolate Citrobacter freundii Strain SL151

Citrobacter freundii is a Gram-negative opportunistic pathogen that is increasingly being recognized as a causative agent of hospital-acquired urinary tract infections and an important reservoir of antimicrobial resistance determinants. In this report, we describe the finished genome sequence of C. freundii strain SL151, a highly multidrug-resistant human urine isolate.

Draft Genome Sequence of Klebsiella pneumoniae KGM-IMP216 Harboring blaCTX-M-15, blaDHA-1, blaTEM-1B, blaNDM-1, blaSHV-28, and blaOXA-1, Isolated from a Patient in Lebanon

We present the draft genome of highly drug-resistant Klebsiella pneumoniae KGM-IMP216, isolated from a urine sample collected from a patient in Lebanon. The draft genome sequence consisted of 77 contigs, including a combined 5,731,500 bases with 57% G+C content.

Horizontal gene transfer in the human gastrointestinal tract: potential spread of antibiotic resistance genes

Bacterial infections are becoming increasingly difficult to treat due to widespread antibiotic resistance among pathogens. This review aims to give an overview of the major horizontal transfer mechanisms and their evolution and then demonstrate the human lower gastrointestinal tract as an environment in which horizontal gene transfer of resistance determinants occurs. Finally, implications for antibiotic usage and the development of resistant infections and persistence of antibiotic resistance genes in populations as a result of horizontal gene transfer in the large intestine will be discussed.