Emergence of a novel mobile colistin resistance gene, mcr-8, in NDM-producing Klebsiella pneumoniae

Identification of an extensively drug-resistant Escherichia coli clinical strain harboring mcr-1 and blaNDM-1 in Korea

The development of colistin resistance in carbapenem-resistant strains poses a serious public health problem. In this study, we collected 249 carbapenem-resistant Escherichia coli isolates from patients in Seoul in 2018, and screened all isolates for colistin resistance and for the presence of mobile colistin resistance (mcr) genes. Colistin-resistant strains were further analyzed using multilocus sequence typing, antimicrobial susceptibility testing, detection of antibiotic resistance determinants, plasmid transconjugation, and whole-genome sequencing. Three of the 249 carbapenem-resistant isolates were resistant to colistin, and mcr-1 was detected in one isolate (SECR18-0888), which belonged to sequence type 156 and was resistant to all antibiotics tested except tigecycline. The mcr-1.1 gene was located on an ~62 kb self-transferable IncI2 plasmid along with the bla_CTX-M-55 gene, and the bla_NDM-1, bla_TEM, qepA1, and rmtB genes were additionally detected in SECR18-0888. As an extensively drug-resistant E. coli strain producing MCR-1 and NDM-1 was identified in Korea for the first time, continued monitoring of colistin resistance in carbapenem-resistant Enterobacteriaceae should be reinforced.

Phenotypic and Genotypic Antimicrobial Resistance in Non-O157 Shiga Toxin-Producing Escherichia coli Isolated From Cattle and Swine in Chile

Non-O157 Shiga toxin-producing Escherichia coli (STEC) is a zoonotic pathogen that causes bloody diarrhea and hemolytic-uremic syndrome in humans, and a major cause of foodborne disease. Despite antibiotic treatment of STEC infections in humans is not recommended, the presence of antimicrobial-resistant bacteria in animals and food constitutes a risk to public health, as the pool of genes from which pathogenic bacteria can acquire antibiotic resistance has increased. Additionally, in Chile there is no information on the antimicrobial resistance of this pathogen in livestock. Thus, the aim of this study was to characterize the phenotypic and genotypic antimicrobial resistance of STEC strains isolated from cattle and swine in the Metropolitan region, Chile, to contribute relevant data to antimicrobial resistance surveillance programs at national and international level. We assessed the minimal inhibitory concentration of 18 antimicrobials, and the distribution of 12 antimicrobial resistance genes and class 1 and 2 integrons in 54 STEC strains. All strains were phenotypically resistant to at least one antimicrobial drug, with a 100% of resistance to cefalexin, followed by colistin (81.5%), chloramphenicol (14.8%), ampicillin and enrofloxacin (5.6% each), doxycycline (3.7%), and cefovecin (1.9%). Most detected antibiotic resistance genes were dfrA1 and tetA (100%), followed by tetB (94.4%), bla_TEM−1 (90.7%), aac(6)-Ib (88.9%), bla_AmpC (81.5%), cat1 (61.1%), and aac(3)-IIa (11.1%). Integrons were detected only in strains of swine origin. Therefore, this study provides further evidence that non-O157 STEC strains present in livestock in the Metropolitan region of Chile exhibit phenotypic and genotypic resistance against antimicrobials that are critical for human and veterinary medicine, representing a major threat for public health. Additionally, these strains could have a competitive advantage in the presence of antimicrobial selective pressure, leading to an increase in food contamination. This study highlights the need for coordinated local and global actions regarding the use of antimicrobials in animal food production.

Genomic Characterization of mcr-1-carrying Salmonella enterica Serovar 4,[5],12:i:- ST 34 Clone Isolated From Pigs in China

Salmonella enterica serovar 4,[5],12:i:-, so-called Typhimurium monophasic variant, has become one of the most frequently isolated serovars both in humans and in animals all over the world. The increasing prevalence of mcr-1-carrying Salmonella poses significant global health concerns. However, the potential role of Salmonella 4,[5],12:i:- in mcr-1 gene migration through the food chain to the human remains obscure. Here, we investigated 337 Salmonella isolates from apparently healthy finishing pigs, which is rarely studied, obtained from pig farms and slaughterhouses in China. The mcr-1 gene was found in four colistin-resistant S. enterica 4,[5],12:i:- isolates. Notably, all four isolates belonged to sequence type 34 (ST34) with multidrug resistance phenotype. Further genomic sequencing and antimicrobial resistance characterization confirmed that mcr was responsible for the colistin resistance, and the conjugation assay demonstrated that three of four isolates carried mcr-1 in IncHI2 plasmid. Importantly, mcr-1 and class-1 integron were found to co-localize in two strains with IncHI2 plasmid. By collecting all the mcr-1-carrying Typhimurium and monophasic variant strains across the food chain (farm animals, animal-origin food, and humans), our phylogenomic analysis of available 66 genomes, including four strains in this study, demonstrated an independent phylogenetic cluster of all eight Chinese swine-originated isolates and one human isolate. Together, this study provides direct evidence for clonal and pork-borne transmission of mcr-1 by Salmonella 4,[5],12:i:- ST34 in China and highlighted a domestication pathway by acquisition of additional antimicrobial resistance determinants in Chinese ST34 isolates.

Quantitative Release Assessment of mcr-mediated Colistin-resistant Escherichia Coli from Japanese Pigs

Colistin is a critically important antibiotic for humans. The Japanese government withdrew colistin growth promoter and shifted therapeutic colistin to a second-choice drug for pigs in 2017. A quantitative release assessment of mcr-mediated colistin-resistant Escherichia coli (E. coli) in Japanese finisher pigs was conducted under the World Organisation for Animal Health (OIE) risk assessment framework. Input data included colistin resistance and mcr-1-5 test results for E. coli isolates in the Japan Veterinary Resistance Monitoring System (JVARM), postal survey results regarding indication disease occurrence and colistin use by swine veterinarians in 2017 and 2018, and colistin resistance and mcr monitoring experiments at four pig farms in 2017-2018. An individual-based model was developed to assess the risk: the proportion of Japanese finisher pigs with mcr-1-5-mediated colistin-resistant E. coli dominant in the gut on an arbitrary day. Before implementing risk management measures, the risk was estimated to be 5.5% (95% CI: 4.2%-10.1%). At 12 months after stopping colistin growth promoter, the proportion of pigs with plasmid-mediated colistin-resistant E. coli declined by 52.5% on the experiment farms (95% CI: 8.7%-80.8%). The probability of therapeutic colistin use at the occurrence of bacterial diarrhea declined from 37.3% (95% CI: 30.3%-42.5%) in 2017 to 31.4% (95% CI: 26.1%-36.9%), and that of edema disease declined from 55.0% (95% CI: 46.0%-63.7%) to 44.4% (95% CI: 36.9%-52.0%). After risk management implementation, the risk was estimated to have declined to 2.3% (95% CI: 1.8%-4.3%; 58.2% reduction). Scenario analyses showed that pen-level colistin treatment effectively reduces the risk from 5.5% to 4.7% (14.5% reduction), an effect similar to stoppage of therapeutic colistin (16.4% reduction to 4.6%).

First report of plasmid-mediated colistin resistance mcr-8.1 gene from a clinical Klebsiella pneumoniae isolate from Lebanon

Colistin is considered as a last resort treatment for infections caused by multidrug-resistant Enterobacteriaceae. Plasmid-mediated mobile colistin resistance (mcr) genes contributed to the global spread of colistin resistance. This is the first report of plasmid-mediated colistin resistance mcr-8 gene from a clinical Klebsiella pneumoniae K9 isolate recovered from Lebanon. The isolate was characterized phenotypically and genotypically through both short and long read whole-genome sequencing, plasmid typing and conjugation assays. k9 belonged to sequence type 15 and harbored 31 antimicrobial resistance genes. The mcr-8.1 variant was carried on a novel ~ 300 kb multireplicon plasmid having IncFIA, IncR and IncHI1B. The plasmid was conjugative and carried a plethora of antimicrobial resistance determinants. The introduction of novel mcr variants in Lebanon poses an alarming health concern. Surveillance and screening for colistin resistant Enterobacteriaceae and mcr in livestock, animal farms, imported meat and poultry is highly recommended along with monitoring antibiotic use.

Genetic Characterization of Carbapenemase-Producing Enterobacter cloacae Complex and Pseudomonas aeruginosa of Food of Animal Origin from Egypt

The increasing spread of carbapenem resistance is a serious global public health concern that negatively affects human and animal health. In this study we characterized the carbapenemase production in gram-negative bacteria isolated from different meat and meat products in Egypt. Phenotypic and genotypic susceptibility testing were investigated. Two Enterobacter cloacae complex strains, isolated from kofta and beef burger, and one Pseudomonas aeruginosa isolated from minced meat, were found to harbor VIM-1 and VIM-2, respectively. These isolates showed multidrug resistance phenotype. The phenotypic carbapenemase production was confirmed with Carba NP test in addition to modified Hodge test, modified carbapenem inactivation method, and ethylenediaminetetraacetic acid inhibition test. The bla_VIM-1 gene in both non-clonally related E. cloacae complex strains was part of a class 1 integron that also carried other resistance gene cassettes such as aacA7, dfrA1, ΔaadA, and smr. This integron was uncommonly disrupted by the insertion sequence ISPa21, located on a self-conjugative plasmid of either the A/C or HI2 incompatibility group with a size of >93 kb. The bla_VIM-2 gene was identified within a class 1 integron, followed downstream by resistance genes aadB and bla_OXA-10. The transfer of bla_VIM-2 gene from P. aeruginosa failed, suggesting that this gene was located on the chromosome. Further studies are needed to screen the dissemination of carbapenemase-producing bacteria in both the environment and food chain.

Difficulty in detecting low levels of polymyxin resistance in clinical Klebsiella pneumoniae isolates: evaluation of Rapid Polymyxin NP test, Colispot Test and SuperPolymyxin medium

Polymyxins are important therapeutic options for treating infections, mainly those caused by carbapenem-resistant Klebsiella pneumoniae. Specific chemical characteristics of polymyxins make it difficult to perform antimicrobial susceptibility testing, especially within the clinical laboratory. Here we aimed to evaluate the performance of three phenotypic methods: Rapid NP Polymyxin Test, ColiSpot test and the SuperPolymyxin medium. To accomplish this, 170 non-duplicate clinical K. pneumoniae isolates were analysed (123 colistin-resistant and 47 susceptible). The sensitivity and specificity obtained for Rapid Polymyxin NP Test, Colispot and SuperPolymyxin medium were, respectively, 90% and 94%, 74% and 100%, and 82% and 85%. Very major errors occurred more frequently in low-level colistin-resistant isolates (MICs 4 and 8 μg/mL). Rapid Polymyxin NP proved to be a method capable of identifying colistin-resistant strains in acceptable categorical agreement. However, major errors and very major errors of this method were considered unacceptable for colistin-resistance screening. Although the Colispot test is promising and easy to perform and interpret, the results did not reproduce well in the isolates tested. The colistin-containing selective medium (SuperPolymyxin) showed limitations, including quantification of mucoid colonies and poor stability. Nevertheless, Colispot and SuperPolymyxin medium methods did not present acceptable sensitivity, specificity and categorical agreement. It is essential to use analytical tools that faithfully reproduce bacterial resistance in vitro, especially in last-line drugs, such as polymyxins, when misinterpretation of a test can result in therapeutic ineffectiveness.

Characterization of a Novel mcr-8.2-Bearing Plasmid in ST395 Klebsiella pneumoniae of Chicken Origin

The emergence of mobile colistin resistance mcr genes undermines the efficacy of colistin as the last-resort drug for multi-drug resistance infections and constitutes a great public health concern. Plasmids play a critical role in the transmission of mcr genes among bacteria. One colistin-resistant Klebsiella pneumoniae strain of chicken origin was collected and analyzed by antimicrobial susceptibility testing, PCR, conjugation assay and S1-PFGE. Whole-genome sequencing (WGS) approach combining Illumina and MinION platforms was utilized to decipher the underlying colistin resistance mechanism and genetic context. A novel mcr-8.2-bearing plasmid p2019036D-mcr8-345kb with 345 655 bp in size encoding various resistance genes including floR, sul1, aadA16, aadA2, bla_CTX-M-27, bla_DHA-1, tet(D), dfrA12 and qnrB4 was identified responsible for the colistin resistance phenotype. Plasmid comparison has shown that the mcr-8.2-bearing plasmid differed from other reported plasmids positive for mcr-8.2 but shared the same core mcr-8.2-bearing conserved region. This study demonstrates the emergence of mcr-8.2-bearing K. pneumoniae of animal origin is a potential risk to humans.

Rate of polymyxin resistance among Acinetobacter baumannii recovered from hospitalized patients: a systematic review and meta-analysis

We conducted a systematic review and meta-analysis to determine the rate of polymyxin resistance among Acinetobacter baumannii isolates causing infection in hospitalized patients around the world during the period of 2010-2019. The systematic review was performed on September 1, 2019, using PubMed/MEDLINE, Scopus, and Web of Science; studies published after January 1, 2010, were selected. The data were summarized in tables, critically analyzed, and treated statistically using the RStudio® Software with Meta package and Metaprop Command. After applying exclusion factors, 41 relevant studies were selected from 969 articles identified on literature search. The overall rate of polymyxin-resistant A. baumannii (PRAB) related to hospitalized patients was estimated to be 13% (95% CI, 0.06-0.27), where a higher rate was observed in America (29%; 95% CI, 0.12-0.55), followed by Europe (13%; 95% CI, 0.02-0.52), and Asia (10%; 95% CI, 0.02-0.32). The extensive use of polymyxins on veterinary to control bacterial infection and growth promotion, as well as the resurgence in prescription and use of polymyxins in the clinics against carbapenem-resistant gram-negative bacteria, may have contributed to the increased incidence of PRAB. The findings of this meta-analysis revealed that the rate of PRAB recovered from hospitalized patients is distinctively high. Thus, action needs to be taken to develop strategies to combat the clinical incidence of PRAB-induced hospital infections.

Plasmid-Determined Colistin Resistance in the North African Countries: A Systematic Review

We have conducted a systematic review to update available information on plasmid-mediated colistin resistance (mobilized colistin resistance [mcr]) genes in North African countries. We have searched the articles of PubMed, Scopus, and Web of Science databases reporting plasmid-mediated colistin resistance bacteria isolated in North African countries. After searching and selection, 30 studies that included 208 mcr-positive isolates were included. Different mcr-positive strains frequencies were recorded and ranged from 2% in clinical isolates to 12.3% in environmental samples. Escherichia coli was the predominant species recorded and these microorganisms showed high resistance to ciprofloxacin and cotrimoxazole. IncHI2 plasmids are probably the key vectors responsible for the dissemination of mcr genes in these countries. This review highlighted that the mcr-positive isolates are circulating in different ecological niches with different frequencies. Therefore, actions should be implemented to prevent the dissemination of the mcr genes within and outside of these countries, such as microbiological and molecular surveillance programs and restriction use of colistin in farming.

Circumventing colistin resistance by combining colistin and antimicrobial peptides to kill colistin-resistant and multidrug-resistant Gram-negative bacteria

Objectives:

Colistin is a ‘last-line’ antibiotic used to treat multidrug-resistant Gram-negative bacteria, but colistin resistance has emerged. Colistin normally binds to the lipid A moiety on the bacterial outer membrane, where it then destroys the bacterial membrane. Mobilize colistin resistance (MCR, encoded by mcr-1 and others) is a phosphoethanolamine transferase that modifies lipid A, preventing colistin binding. We hypothesized that combining pore-forming AMPs and colistin will circumvent this mechanism and reduce the minimum inhibitory concentration (MIC) of colistin for both colistin- and multidrug-resistant Gram-negative bacteria.

Methods:

In vitro cultures were incubated for 18 h after combining bacteria (Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii and Pseudomonas aeruginosa) with serially diluted colistin and a fixed concentration of peptide MSI-78 or OTD-244.

Results:

When combined with either peptide, the colistin MIC decreased more than 4-fold for 88% of all tested isolates (n = 17; range, 4–64-fold reduction) and for 75% of colistin-resistant isolates (n = 8; range, 4–64-fold reduction). The concentrations used had no effect on red blood cells based on a conventional haemolysis assay.

Conclusions:

These findings are consistent with two membrane-damaging compounds having an additive effect on bacterial killing. Combining antimicrobial peptides with colistin is a promising strategy for bypassing MCR-mediated colistin resistance, but also for improving the susceptibility of other Gram-negative bacteria while potentially reducing the therapeutic concentration of colistin needed to treat infections.

Characterization of the global distribution and diversified plasmid reservoirs of the colistin resistance gene mcr-9

The emergence and spread of mobilized colistin resistance (mcr) genes have triggered extensive concerns worldwide. Here, we characterized the global distribution of mcr-9, a newly-identified variant of mcr, by assembling the data set of mcr-9-positive isolates from GenBank database and the literature available. Genetic features of all the mcr-9-harboring plasmids were determined by bioinformatic analysis. We showed that mcr-9 is globally distributed in 21 countries across six continents, with a wide dissemination among various species of Enterobacteriaceae strains from human, animal, food and environment. IncHI2-ST1 plasmids were found to be the predominant replicon type carrying mcr-9. Comparative genomics highlighted that IncHI2-type plasmids may also serve as a critical reservoir of mcr-9, from which different types of circulating plasmids acquired the mcr-9. Results revealed that the rcnR-rcnA-pcoE-pcoS-IS903-mcr-9-wbuC structure was consistent in most mcr-9 cassettes, suggesting a relatively unitary model involved in the mobilization of mcr-9. It is most likely that the spread of mcr-9 was mainly attributed to the conjugation and recombination events of mcr-9-carrying plasmids. In summary, our results provide a comprehensive picture of the distribution and genetic environment of mcr-9, and demonstrate the central roles played by IncHI2 plasmids in the worldwide dissemination of mcr-9.

Co-Occurrence of mcr-9 and bla NDM-1 in Enterobacter cloacae Isolated from a Patient with Bloodstream Infection

Background

Bloodstream infection (BSI) caused by carbapenem-resistant Enterobacteriaceae are potentially life-threatening related to poorer outcomes. Colistin is considered one of the last-resort treatments against human infections caused by multidrug-resistant (MDR) Gram-negative bacteria. Therefore, emergence of strains from the blood that co-harboring mcr and carbapenem resistance genes were considered as a serious problem.

Purpose

In this study, two mcr-9-harboring MDR Enterobacter cloacae isolates BSI034 and BSI072 recovered from BSI patients were identified, one of which co-harbored mcr-9 and bla_NDM-1. The genetic characteristics of the MDR plasmid needed to be clarified.

Methods

S1-PFGE and Southern blotting were conducted to determine the location of mcr-9. Whole-genome sequencing was performed to obtain the complete genome and plasmid sequences. The resistome and virulence genes of the strains, accompanied by the genetic characteristics of mcr-9- and bla_NDM-1-harboring plasmids, were analyzed.

Results

Whole-genome sequencing showed that BSI034 harbored mcr-9-carrying IncHI2-type pBSI034-MCR9 and bla_NDM-1-carrying IncX3-type pBSI034-NDM1. The 278,517 bp pBSI034-MCR9 carried mcr-9 along with the other 19 resistance genes. mcr-9 was flanked by IS903B (1057 bp) and IS26 (820 bp) in the same orientation. In addition to resistance genes, strain BSI034 also carried a chromosome-located Yersinia high-pathogenicity island, which harbored genes of yersiniabactin biosynthesis operon ybtSXQPAUTE, irp1/2, and fyuA.

Conclusion

We described the complete genome and mcr-9/bla_NDM-1-co-harboring plasmid of E. cloacae from a BSI patient. Notable differences were observed within mosaic modules between pBSI034-MCR9 and other mcr-9-harboring plasmids due to extensive recombination via horizontal gene transfer.

What's new in mechanisms of antibiotic resistance in bacteria of clinical origin?

The discovery, commercialization and administration of antibiotics revolutionized the world of medicine in the middle of the last century, generating a significant change in the therapeutic paradigm of the infectious diseases. Nevertheless, this great breakthrough was soon threatened due to the enormous adaptive ability that bacteria have, through which they are able to develop or acquire different mechanisms that allow them to survive the exposure to antibiotics. We are faced with a complex, multifactorial and inevitable but potentially manageable threat. To fight against it, a global and multidisciplinary approach is necessary, based on the support, guidance and training of the next generation of professionals. Nevertheless, the information published regarding the resistance mechanisms to antibiotics are abundant, varied and, unfortunately, not always well structured. The objective of this review is to structure the, in our opinion, most relevant and novel information regarding the mechanisms of resistance to antibiotics that has been published from January 2014 to September 2019, analysing their possible clinical and epidemiological impact.

Antimicrobial resistance profile and prevalence of extended-spectrum beta-lactamases (ESBL), AmpC beta-lactamases and colistin resistance (mcr) genes in Escherichia coli from swine between 1999 and 2018

The frequent usage of antibiotics in livestock has led to the spread of resistant bacteria within animals and their products, with a global warning in public health and veterinarians to monitor such resistances. This study aimed to determine antibiotic resistance patterns and genes in pig farms from Spain during the last twenty years. Susceptibility to six antibiotics commonly used in pig production was tested by qualitative (disk diffusion) and quantitative (minimum inhibitory concentration, MIC) methods in 200 strains of Escherichia coli which had been isolated between 1999 and 2018 from clinical cases of diarrhoea in neonatal and post-weaned piglets. Results showed resistance around 100% for amoxicillin and tetracycline since 1999, and a progressive increase in ceftiofur resistance throughout the studied period. For colistin, it was detected a resistance peak (17.5% of the strains) in the 2011–2014 period. Concerning gentamicin, 11 of 30 strains with intermediate susceptibility by the disk diffusion method were resistant by MIC. Besides, the most frequent antimicrobial resistance genes were the extended-spectrum beta-lactamase (ESBL) bla_CTX-M (13.5% of strains, being CTX-M-14, CTX-M-1 and CTX-M-32 the most prevalent genomes, followed by CTX-M-27, CTX-M-9 and CTX-M-3), AmpC-type beta-lactamase (AmpC) bla_CMY-2 (3%) and colistin resistance genes mcr-4 (13%), mcr-1 (7%) and in less proportion mcr-5 (3%). Interestingly, these mcr genes were already detected in strains isolated in 2000, more than a decade before their first description. However, poor concordance between the genotypic mcr profile and the phenotypical testing by MIC was found in this study. These results indicate that although being a current concern, resistance genes and therefore antimicrobial resistant phenotypes were already present in pig farms at the beginning of the century.

Antimicrobial Resistance of Commensal Escherichia coli Isolated from Food Animals in Qatar

Objectives: This study aims at evaluating the phenotypic and genotypic antimicrobial resistance (AMR) patterns of 18 clinically relevant antibiotics in food animals in Qatar. Materials and Methods: Fecal samples from camels, cattle, and pigeons (300) were collected from different slaughterhouses and farms. Escherichia coli isolates were recovered on selective media, confirmed biochemically, and tested for antibiotic susceptibility using a disk diffusion assay. Any isolate that showed resistance to colistin was confirmed using the E-test and polymerase chain reaction for mcr genes. Results: Overall, a total of 88.7% (n = 266/300) recovery rate was achieved from all samples. Resistance to at least one antibiotic was recorded in 70.7% of pigeons, 37.2% of cattle, and only 20.8% of camel samples. Multidrug resistance (MDR) was highest in isolates from pigeons, 50% (n = 44). Moreover, trimethoprim/sulfamethoxazole (an antibiotic used to treat a variety of bacterial infections) resistance was present in 22.2% (n = 59) of all E. coli isolates. Only one E. coli isolate from a pigeon showed resistance to colistin (mcr-1 gene encoded), a drug of last resort in human medicine against gram-negative bacterial infection. Conclusions: We previously reported high multidrug resistance of E. coli in chickens, with significant resistance to colistin. We observed a lower AMR profile in ruminants. The high resistance profile observed in pigeons (70.7%), including high multidrug resistance (50%), is alarming as these animals could rapidly disseminate resistant bacteria to various locations. Continuous monitoring of AMR in livestock in Qatar is necessary toward introducing an antimicrobial stewardship program and control of antibiotic usage in the veterinary sector.

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.

Emergence of Mobile Colistin Resistance (mcr-8) in a Highly Successful Klebsiella pneumoniae Sequence Type 15 Clone from Clinical Infections in Bangladesh

The emergence of mobilized colistin resistance genes (mcr) has become a serious concern in clinical practice, compromising treatment options for life-threatening infections. In this study, colistin-resistant Klebsiella pneumoniae harboring mcr-8.1 was recovered from infected patients in the largest public hospital of Bangladesh, with a prevalence of 0.3% (3/1,097). We found mcr-8.1 in an identical highly stable multidrug-resistant IncFIB(pQil) plasmid of ∼113 kb, which belonged to an epidemiologically successful K. pneumoniae clone, ST15. The resistance mechanism was proven to be horizontally transferable, which incurred a fitness cost to the host. The core genome phylogeny suggested the clonal spread of mcr-8.1 in a Bangladeshi hospital. Core genome single-nucleotide polymorphisms among the mcr-8.1-positive K. pneumoniae isolates ranged from 23 to 110. It has been hypothesized that mcr-8.1 was inserted into IncFIB(pQil) with preexisting resistance loci, bla _TEM-1b and bla _CTX-M-15, by IS903B Coincidentally, all resistance determinants in the plasmid [mcr-8.1, ampC, sul2, 1d-APH(6), APH(3'')-Ib, bla _TEM-1b, bla _CTX-M-15] were bracketed by IS903B, demonstrating the possibility of intra- and interspecies and intra- and intergenus transposition of entire resistance loci. This is the first report of an mcr-like mechanism from human infections in Bangladesh. However, given the acquisition of mcr-8.1 by a sable conjugative plasmid in a successful high-risk clone of K. pneumoniae ST15, there is a serious risk of dissemination of mcr-8.1 in Bangladesh from 2017 onwards.IMPORTANCE There is a marked paucity in our understanding of the epidemiology of colistin-resistant bacterial pathogens in South Asia. A report by Davies and Walsh (Lancet Infect Dis 18:256-257, https://doi.org/10.1016/S1473-3099(18)30072-0, 2018) suggests the export of colistin from China to India, Vietnam, and South Korea in 2016 was approximately 1,000 tons and mainly used as a poultry feed additive. A few reports forecast that the prevalence of mcr in humans and livestock will increase in South Asia. Given the high prevalence of bla _CTX-M-15 and bla _NDM in India, Bangladesh, and Pakistan, colistin has become the invariable option for the management of serious infections, leading to the emergence of mcr-like mechanisms in South Asia. Systematic scrutiny of the prevalence and transmission of mcr variants in South Asia is vital to understanding the drivers of mcr genes and to initiate interventions to overcome colistin resistance.

Farm animals and aquaculture: significant reservoirs of mobile colistin resistance genes

Colistin resistance has attracted substantial attention after colistin was considered as a last-resort drug for the treatment of infections caused by carbapenem-resistant and/or multidrug-resistant (MDR) Gram-negative bacteria in clinical settings. However, with the discovery of highly mobile colistin resistance (mcr) genes, colistin resistance has become an increasingly urgent issue worldwide. Despite many reviews, which summarized the prevalence, mechanisms, and structures of these genes in bacteria of human and animal origin, studies on the prevalence of mobile colistin resistance genes in aquaculture and their transmission between animals and humans remain scarce. Herein, we review recent reports on the prevalence of colistin resistance genes in animals, especially wildlife and aquaculture, and their possibility of transmission to humans via the food chain. This review also gives some insights into the routine surveillance, changing policy and replacement of polymyxins by polymyxin derivatives, molecular inhibitors, and traditional Chinese medicine to tackle colistin resistance.

Emerging colistin resistance in Salmonella enterica serovar Newport isolates from human infections

Worldwide emergence of Salmonella enterica serovar Newport (S. Newport) infection in humans, in parallel with a significant increasing prevalence of antimicrobial resistance (AR), is a serious public health concern. However, the prevalence of S. Newport resistance in China remains largely unknown. A retrospective study of 287 S. Newport clinical isolates collected during 1997-2018 was undertaken for characterization of AR profiles using the micro-dilution assay. We found a recent emergence of colistin resistance in four Chinese clinical isolates, including mcr-1-positive isolates. Importantly, phylogenomic and microbiological investigations indicate multiple independent clonal transmission of colistin-resistant S. Newport isolates of different seafood origins. Our study highlights potential reservoirs for transmission of colistin resistance and suggests that the global food supply chain may facilitate this dissemination.

Identification of novel mobile colistin resistance gene mcr-10

Mobile colistin resistance (mcr) genes represent an emerging challenge. Here we describe a novel mcr gene, mcr-10, on an IncFIA plasmid of an Enterobacter roggenkampii clinical strain. mcr-10 has the highest nucleotide identity (79.69%) with mcr-9 and encodes MCR-10 with 82.93% amino acids identical to MCR-9. mcr-10 confers 4-fold increase in colistin MIC (from 1 to 4 mg/L) when cloned into a colistin-susceptible E. roggenkampii strain. By screening GenBank, mcr-10 was found in various Enterobacteriaceae species of countries in four continents, suggesting that this gene has widely spread. MCR-10 shows 79.04% to 83.67% amino acid identity and highly conserved predicted protein structures with chromosomally encoded MCR-like phosphoethanolamine transferases (designated MCR-B here) of various Buttiauxella species. MCR-10, MCR-9 and MCR-B proteins may, therefore, originate from a common ancestor. mcr-10 was adjacent to a site-specific recombinase-encoding gene and was bracketed by IS903 and may be mobilized by site-specific recombination or composite transposon. Our results indicate that mcr-10 is a novel plasmid-borne colistin resistance gene and warrants immediate monitoring and further studies.

Phenotypic Detection of Plasmid-Mediated Colistin Resistance in Enterobacteriaceae

The aim of this work was to evaluate an easy-to-perform assay based upon inhibition of mobile colistin resistance (MCR) activity by EDTA. We included 92 nonrelated isolates of Enterobacteriaceae (74 Escherichia coli, 17 Klebsiella pneumoniae, and 1 Serratia marcescens). Our proposed method is based on a modification of the colistin agar-spot screening test (CAST), a plate containing 3 μg/ml colistin, by adding an extra plate of colistin agar-spot supplemented with EDTA (eCAST). Bacterial growth was evaluated after 24 h of incubation at 35°C. All the colistin-resistant isolates showed development on the CAST plates. Colistin-resistant K. pneumoniae without mcr-1 and S. marcescens also grew on the eCAST plates. In contrast, colistin-resistant MCR-producing E. coli was not able to grow in eCAST plates. The combined CAST/eCAST test could provide a simple and easy-to-perform method to differentiate MCR-producing Enterobacteriaceae from those in which colistin resistance is mediated by chromosomal mechanisms.

Epidemiology of colistin-resistant, carbapenemase-producing Enterobacteriaceae and Acinetobacter baumannii in Croatia

Colistin is a last-resort antibiotic for the treatment of infections caused by multidrug and carbapenem-resistant Gram-negative bacteria. Colistin resistance has been emerging and multiple outbreaks have been reported in Europe and elsewhere. It has been most frequently reported in carbapenem-resistant K. pneumoniae. In this study, 24 multidrug and colistin-resistant clinical isolates (14 K. pneumoniae, one E. aerogenes, one E. cloacae, and eight A. baumannii) were collected from four hospitals in Croatia from 2013 to 2018, in order to analyse the molecular epidemiology and mechanisms of antibiotic resistance. β-lactamase and carbapenemase genes were detected by PCR. Genotyping was done on selected isolates by rep-PCR. Whole genome sequencing (WGS) was performed to discover possible molecular mechanisms for the observed colistin resistance. All isolates, except two K. pneumoniae isolates, were extensively drug resistant. Ten out of 16 (63%) K. pneumoniae isolates possessed bla_OXA-48, which is the most common carbapenem resistance gene in Croatia and in other parts of Europe. All A. baumannii isolates possessed the OXA-23-like carbapenem hydrolysing oxacillinase and five turned out to be pandrug-resistant. Colistin resistance was most likely chromosomally mediated. After sequence analysis, none of the isolates were found to possess any of the mcr gene variants. Several previously reported mutations were found in PmrB, PhoP, PhoQ, and MgrB, which are associated with colistin resistance. In the global phylogenetic analysis, DNA mutations causing mutations in the MgrB protein were present mostly in lineages comprising colistin resistant isolates, and the second most prevalent mutation (K3X) was also encountered in our isolates. In addition, based on genotyping by rep-PCR, the spread of colistin resistance is most likely to be clonal. Most importantly, the presence of colistin resistance together with carbapenemase genes in extensively drug resistant isolates poses real threats in the use of carbapenems and colistin to fight infections.

Retrospective Screening and Analysis of mcr-1 and bla NDM in Gram-Negative Bacteria in China, 2010-2019

Currently, Gram-negative bacteria have developed multidrug and broad-spectrum drug resistance, and the numbers of species and strains carrying mcr or bla_NDM genes are increasing. In this study, mcr-1 and bla_NDM distribution of 12,858 Gram-negative bacteria isolated from wildlife, patients, livestock, poultry and environment in 14 provinces of China from 2010 to 2019 and the antibiotics resistance in regard to polymyxins (polymyxin B and colistin) and carbapenems of positive strains were investigated. A total of 70 strains of 10 species carried the mcr-1 gene, positive rates of patients, livestock and poultry, and environmental strains were 0.62% (36/5,828), 4.07% (29/712), 5.43% (5/92), respectively. Six strains of 3 species carrying the bla_NDM gene all came from patients 0.10% (6/5,828). Two new mcr-1 gene variants (GenBank: MK965883, MK965884) were identified, one of which contains premature stop codon. The drug susceptibility results showed that all mcr-1 carriers were sensitive to carbapenems, among which, 66 strains were resistant and 4 were sensitive to polymyxins. The strains with the bla_NDM gene had different degrees of resistance to carbapenems and were sensitive to polymyxins. The findings that species carrying mcr-1 or bla_NDM genes were limited and mostly normal flora of opportunistic or low pathogenic organisms indicated that transfer of mcr-1 and bla_NDM genes between bacteria was relatively limited in China. The none detection among wildlife compared with other sources supports the speculation that the emergence of and increase in polymyxins and carbapenem-resistant strains was mainly related to the selective pressure of antibiotics.

Development of a Novel mcr-6 to mcr-9 Multiplex PCR and Assessment of mcr-1 to mcr-9 Occurrence in Colistin-Resistant Salmonella enterica Isolates From Environment, Feed, Animals and Food (2011-2018) in Germany

The polymyxin antibiotic colistin has been used in decades for treatment and prevention of infectious diseases in livestock. Nowadays, it is even considered as last-line treatment option for severe human infections caused by multidrug- and carbapenem-resistant Gram-negative bacteria. Therefore, the discovery of plasmid-mediated mobile colistin resistance (mcr) genes raised major public health concern. The aim of our study was to analyze colistin-resistant Salmonella enterica strains from animals, food, feed and the environment collected at the National Reference Laboratory for Salmonella in Germany on the presence of mcr-1 to mcr-9 genes. Altogether 407 colistin-resistant (MIC >2 mg/L) Salmonella isolates received between 2011 and 2018 were selected and screened by PCR using a published mcr-1 to mcr-5 as well as a newly developed mcr-6 to mcr-9 multiplex PCR protocol. 254 of 407 (62.4%) isolates harbored either mcr-1 (n = 175), mcr-4 (n = 53), mcr-5 (n = 18) or mcr-1 and mcr-9 (n = 8). The number of mcr-positive isolates ranged from 19 (2017) to 64 (2012) per year. WGS revealed that none of our isolates harbored the mcr-9.1 gene. Instead, two novel mcr-9 variants were observed, which both were affected by frameshift mutations and are probably non-functional. The mcr-harboring isolates were mainly derived from animals (77.2%) or food (20.1%) and could be assigned to ten different Salmonella serovars. Many of the isolates were multidrug-resistant. Co-occurrence of mcr-1 and AmpC or ESBL genes was observed in eight isolates. Our findings suggest that mcr genes are widely spread among colistin-resistant Salmonella isolates from livestock and food in Germany. Potential transfer of mcr-harboring isolates along the food chain has to be considered critically.

Probiotics in Animal Husbandry: Applicability and Associated Risk Factors

Probiotics have been emerging as a safe and viable alternative to antibiotics for increasing performance in livestock. Literature was collated via retrieved information from online databases, viz, PubMed, MEDLINE, ScienceDirect, Scopus, Web of Science and Google Scholar. Besides improved immunomodulation and nutrient digestibility, in-feed probiotics have shown drastic reductions in gastrointestinal tract-invading pathogens. However, every novel probiotic strain cannot be assumed to share historical safety with conventional strains. Any strain not belonging to the wild-type distributions of relevant antimicrobials, or found to be harbouring virulence determinants, should not be developed further. Modes of identification and the transmigration potential of the strains across the gastrointestinal barrier must be scrutinized. Other potential risk factors include the possibility of promoting deleterious metabolic effects, excessive immune stimulation and genetic stability of the strains over time. Adverse effects of probiotics could be strain specific, depending on the prevailing immunological and physiological condition of the host. The most crucial concern is the stability of the strain. Probiotics stand a good chance of replacing antibiotics in animal husbandry. The possibility of the probiotics used in animal feed cross-contaminating the human food chain cannot be downplayed. Thus, the established safety measures in probiotic development must be adhered to for a successful global campaign on food safety and security.

The characterization of mobile colistin resistance (mcr) genes among 33 000 Salmonella enterica genomes from routine public health surveillance in England

To establish the prevalence of mobile colistin resistance (mcr) genes amongst Salmonella enterica isolates obtained through public health surveillance in England (April 2014 to September 2017), 33 205 S. enterica genome sequences obtained from human, food, animal and environmental isolates were screened for the presence of mcr variants 1 to 8. The mcr-positive genomes were assembled, annotated and characterized according to plasmid type. Nanopore sequencing was performed on six selected isolates with putative novel plasmids, and phylogenetic analysis was used to provide an evolutionary context for the most commonly isolated clones. Fifty-two mcr-positive isolates were identified, of which 32 were positive for mcr-1, 19 for mcr-3 and 1 for mcr-5. The combination of Illumina and Nanopore sequencing identified three novel mcr-3 plasmids and one novel mcr-5 plasmid, as well as the presence of chromosomally integrated mcr-1 and mcr-3. Monophasic S. enterica serovar Typhimurium accounted for 27/52 (52 %) of the mcr-positive isolates, with the majority clustering in clades associated with travel to Southeast Asia. Isolates in these clades were associated with a specific plasmid range and an additional extended-spectrum beta-lactamase genotype. Routine whole-genome sequencing for public health surveillance provides an effective screen for novel and emerging antimicrobial determinants, including mcr. Complementary long-read technologies elucidated the genomic context of resistance determinants, offering insights into plasmid dissemination and linkage to other resistance genes.

Molecular epidemiology of mcr gene group

Colistin and polymyxin B are the “last reserve” antimicrobials for the treatment of extensively drug-resistant Gram-negative bacterial infections. The rapidly increasing prevalence of polymyxin resistance mediated by the mcr gene localized on plasmid DNA currently poses a high epidemiological threat. In order to control a distribution of mcr genes, it is necessary to develop highly accurate, highly sensitive and easy-to-use diagnostic tools. This paper provides a review of the most relevant studies on the molecular epidemiology as well as current approaches to microbiological and molecular detection of mcr group genes.

Recent progress on elucidating the molecular mechanism of plasmid-mediated colistin resistance and drug design

Antibiotic resistance is a growing global challenge to public health. Polymyxin is considered to be the last-resort antibiotic against most gram-negative bacteria. Recently, discoveries of a plasmid-mediated, transferable mobilized polymyxin resistance gene (mcr-1) in many countries have heralded the increased threat of the imminent emergence of pan-drug-resistant super bacteria. MCR-1 is an inner membrane protein that enables bacteria to develop resistance to polymyxin by transferring phosphoethanolamine to lipid A. However, the mechanism associated with polymyxin resistance has yet to be elucidated, and few drugs exist to address this issue. Here, we review our current understanding regarding MCR-1 and small molecule inhibitors to provide a detailed enzymatic mechanism of MCR-1 and the associated implications for drug design.

Dissemination and Comparison of Genetic Determinants of mcr-Mediated Colistin Resistance in Enterobacteriaceae via Retailed Raw Meat Products

The global food chain may significantly promote the dissemination of bacteria resistant to antibiotics around the world. This study was aimed at determining the prevalence and genetic characteristics of Enterobacteriaceae with mcr-mediated colistin (CT) resistance in retail meat of different origins. Bacteria of the Enterobacteriaceae family carrying the mcr-1 gene were detected in 21% (18/86) of the examined samples, especially in turkey meat and liver originating from EU and non-EU countries (19%) and in rabbit meat imported from China (2%). The examined samples of the meat and liver of chicken and other poultry and of pork and beef were negative for the presence of bacteria carrying the mcr-1 to mcr-5 genes. A huge number of isolates belonging to Escherchia coli (n = 54), Klebsiella pneumoniae (n = 6), and Citrobacter braakii (n = 1) carrying the mcr-1 gene were obtained. Despite the high heterogeneity of the tested isolates, the mcr-1 gene was localized on only three types of plasmids (IncX4, IncHI2, and IncI2). The most frequent type of plasmid was IncX4, which carried the mcr-1 gene in 77% of E. coli and K. pneumoniae isolates from turkey meat and liver samples from the Czechia, Germany, Poland, and Brazil. Our findings indicate highly probable interspecies transfer of IncX4 and IncI2 plasmids within one meat sample. The co-resistance of plasmid-mediated CT resistance encoded by the mcr-1 and ESBL genes was detected in 18% of the isolates. Another noteworthy finding was the fosA3 gene coding for fosfomycin resistance in a multidrug-resistant isolate of E. coli from rabbit meat imported from China. The observed high level of Enterobacteriaceae with plasmids carrying the mcr-1 gene in retail meat reflects the need for Europe-wide monitoring of mcr-mediated CT resistance throughout the whole food chain.

Emergence of colistin resistance in multidrug-resistant Klebsiella pneumoniae and Escherichia coli strains isolated from cancer patients

BACKGROUND

Colistin resistance is mainly driven by alterations in the Gram-negative outer membrane lipopolysaccharides and is caused, in most cases, by mutations in mgrB gene. However, the recent emergence of plasmid-encoded colistin resistance among Enterobacteriaceae strains represents a serious threat to global public health. In this paper we have investigated the rates of colistin resistance and the underlying mechanisms in 450 Klebsiella pneumoniae and Escherichia coli isolates obtained from cancer patients in Egypt.

METHODS

Colistin susceptibility and minimum inhibitory concentrations were determined according to the European Committee on Antimicrobial Susceptibility Testing, by broth microdilution, and by E-test. The mcr-1, mcr-2 and mgrB genes were detected by PCR and then sequenced. Clonal diversity in colistin-resistant K. pneumoniae was evaluated by multilocus sequence typing.

RESULTS

Forty (8.8%) colistin-resistant isolates, including 22 K. pneumoniae and 18 E. coli, were isolated over 18 months. Of these, 50% were carbapenem-resistant, out of which nine were blaOXA-48 and seven blaNDM-1 positive. The mechanisms of colistin resistance could be revealed only in three of the 40 resistant strains, being represented by mcr-1 in one blaNDM-1-positive E. coli strain and in one K. pneumoniae ST11 and by mgrB mutations, detected in one K. pneumoniae isolate. None of the studied isolates harbored mcr-2.

CONCLUSIONS

Our results demonstrate a high frequency of colistin resistance in enterobacterial strains isolated from cancer patients, but a low prevalence of the most well known resistance mechanisms.

Increasing Prevalence of ESBL-Producing Multidrug Resistance Escherichia coli From Diseased Pets in Beijing, China From 2012 to 2017

We investigated antimicrobial resistance trends and characteristics of ESBL-producing Escherichia coli isolates from pets and whether this correlates with antibiotic usage in the clinic. Clinical samples containing E. coli from diseased cats and dogs were screened for antibiotic sensitivity and associated genotypic features. We identified 127 E. coli isolates from 1886 samples from dogs (n = 1565) and cats (n = 321) with the majority from urinary tract infections (n = 108, 85%). High rates of resistance were observed for β-lactams and fluoroquinolones and resistance to > 3 antibiotic classes (MDR) increased from 67% in 2012 to 75% in 2017 (P < 0.0001). This was especially true for strains resistant to 6-9 antibiotics that increased from 26.67 to 60.71%. Increased rates in β-lactam use for clinical treatment accompanied these increasing resistance rates. Accordingly, the most frequently encountered subtypes were bla _CTX-M (n = 44, 34.65%), bla _CTX-M-65 (n = 19) and bla _CTX-M-15 (n = 18) and qnrB (n = 119, 93.70%). The bla _CTX-M-isolates possessed 36 unique pulsed field electrophoretic types (PFGEs) and 28 different sequence types (STs) in ST405 (7, 15.9%), ST131 (3, 6.8%), ST73, ST101, ST372, and ST827 (2, 4.5% each) were the most prevalent. This data demonstrated a high level of diversity for the bla _CTX-M-positive E. coli isolates. Additionally, bla _NDM-5 was detected in three isolates (n = 3, 2.36%), comprised of two ST101 and one ST405 isolates, and mcr-1 was also observed in three colistin-resistant E. coli with three different STs (ST6316, ST405, and ST46). Our study demonstrates an increasing trend in MDR and ESBL-producing E. coli and this correlated with β-lactam antibiotic usage for treatment of these animals. This data indicates that there is significant risk for the spread of resistant bacteria from pets to humans and antibiotic use for pets should be more strictly regulated.

Prevalence of Genes Involved in Colistin Resistance in Acinetobacter baumannii: First Report from Iraq

Background and Aim: Colistin is increasingly being used as a "last-line" therapy to treat infections caused by multidrug-resistant (MDR) Acinetobacter baumannii isolates, when essentially no other options are available in these days. The aim of this study was to detect genes associated with colistin resistance in A. baumannii. Methods: One hundred twenty-one isolates of A. baumannii were collected from clinical and environmental samples during 2016 to 2018 in Baghdad. Isolates were diagnosed as A. baumannii by using morphological tests, Vitek-2 system, 16SrRNA PCR amplification, and sequencing. Antibiotic susceptibility test was carried out using disk diffusion method. Phenotypic detection of colistin resistance was performed by CHROMagar™ COL-APSE medium and broth microdilution method for the determination of the minimal inhibitory concentration. Molecular detection of genes responsible for colistin resistance in A. baumannii was performed by PCR. Results: Ninety-two (76%) of the 121 A. baumannii isolates were colistin resistant. Twenty-six (21.5%) of the 121 isolates showed positive growth on CHROMagar Acinetobacter base for MDR. PCR detected mcr-1, mcr-2, and mcr-3 genes in 89 (73.5%), 78 (64.5%), and 82 (67.8%) A. baumannii isolates, respectively. Seventy-eight (64.5%) of the 121 isolates harbored the integron intI2 gene and 81 (66.9%) contained intI3 gene. Moreover, 60 (49.6%) of the 121 isolates were positive for the quorum sensing lasI gene. Conclusion: The presence of a large percentage of colistin-resistant A. baumannii strains in Baghdad may be due to the presence of mobile genetic elements, and it is urgent to avoid unnecessary clinical use of colistin.

Emergence of colistin-resistant Klebsiella pneumoniae in Poland

In recent years, colistin has been the drug of choice for treatment of nosocomial infections, especially in bloodstream infections, lower respiratory tract infections, or urinary tract infections. In this study, 65 multidrug-resistant Klebsiella pneumoniae isolated from different clinical samples were included. Minimum inhibitory concentration (MIC) of colistin was detected by broth microdilution method in three different ways. For selected K. pneumoniae strains, eazyplex SuperBug mcr-1 test was performed. This test detects mcr-1 gene, which encodes a colistin-resistance determinant. Most of the analyzed K. pneumoniae strains were resistant to colistin in all applied methods. The exception was two strains, where MIC of colistin was 2 mg/L in SensiTest Colistin and MIC-Strip Colistin tests. In MIC COL test, MIC for these strains was 4 mg/L. All analyzed strains produced extended-spectrum beta-lactamases and 11 (16.9%) metallo-beta-lactamases. Eleven (16.9%) K. pneumoniae strains were resistant to all antibiotics, whereas 17 (26.1%) were susceptible to only one drug. Colistin MIC values varied from 2 to >64 mg/L in MIC-Strip Colistin test; from 2 to >16 mg/L in SensiTest Colistin and from 4 to >16 mg/L in MIC COL test. None of the analyzed K. pneumoniae strains carried mcr-1 gene. Data of this work suggest that resistance to colistin emerged among multidrug-resistant K. pneumoniae strains. The tests allowed for reliable estimation of susceptibility to colistin and could be used in microbiological diagnostics.

Colistin Resistance in Enterobacterales Strains - A Current View

Colistin is a member of cationic polypeptide antibiotics known as polymyxins. It is widely used in animal husbandry, plant cultivation, animal and human medicine and is increasingly used as one of the last available treatment options for patients with severe infections with carbapenem-resistant Gram-negative bacilli. Due to the increased use of colistin in treating infections caused by multidrug-resistant (MDR) bacteria, the resistance to this antibiotic ought to be monitored. Bacterial resistance to colistin may be encoded on transposable genetic elements (e.g. plasmids with the mcr genes). Thus far, nine variants of the mcr gene, mcr-1 – mcr-9, have been identified. Chromosomal resistance to colistin is associated with the modification of lipopolysaccharide (LPS). Various methods, from classical microbiology to molecular biology methods, are used to detect the colistin-resistant bacterial strains and to identify resistance mechanisms. The broth dilution method is recommended for susceptibility testing of bacteria to colistin.

Molecular Epidemiological Insights into Colistin-Resistant and Carbapenemases-Producing Clinical Klebsiella pneumoniae Isolates

Purpose

Carbapenemases-producing Klebsiella pneumoniae are challenging antimicrobial therapy of hospitalised patients, which is further complicated by colistin resistance. This study describes molecular epidemiological insights into colistin-resistant and carbapenemases-producing clinical K. pneumoniae.

Patients and methods

Cultures collected from 26 hospitalised patients during 2014-2017 in the main hospital in Molise Region, central Italy, were characterized. The minimum inhibitory concentration for 19 antibiotics was determined, including carbapenems and colistin. Prevalence of resistance-associated genes was investigated through PCR, detecting bla _KPC, bla _GES, bla _VIM, bla _IMP, bla _NDM, bla _OXA-48, bla _CTX-M, bla _TEM, bla _SHV, and mcr-1,2,3,4,5,6,7,8. The mgrB gene was also analysed in colistin-resistant strains by PCR and sequencing assays. K. pneumoniae were typed by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST).

Results

Twenty out of 26 K. pneumoniae were phenotypically resistant to carbapenems and 19 were resistant to colistin. All isolates harbored bla _KPC, and bla _SHV, bla _TEM and bla _VIM were further the most common resistance-associated genes. In colistin-resistant strains, mcr-1,2,3,4,5,6,7,8 variants were not detected, while mutations and insertion elements in mgrB were observed in 68.4% (n=13) in 31.6% (n=6) isolates, respectively. PFGE revealed 12 clusters and 18 pulsotypes at 85% and 95% cut-off, while the Sequence Types ST512 (n=13, 50%), ST101 (n=10, 38.5%), ST307 (n=2, 7.7%) plus a novel ST were detected using MLST.

Conclusion

All K. pneumoniae showed a multidrug-resistant phenotype, particularly to carbapenems and colistin. According to national data, bla _KPC was the prevailing carbapenemase, followed by bla _VIM, while bla _TEM and bla _SHV were among the most frequent beta-lactamases. Consistent with previous reports in Italy, ST512 was the most common clone, particularly during 2014-15, whilst ST101 became dominant in 2016-17. Colistin resistance was mainly associated with deleterious mutations and transposon in the mgrB gene. Improvements of surveillance, compliance with infection prevention procedures and antimicrobial stewardship are essential to limit the spread of resistant K. pneumoniae.

Detection of Colistin Resistance in Escherichia coli by Use of the MALDI Biotyper Sirius Mass Spectrometry System

Polymyxin antibiotics are a last-line treatment for multidrug-resistant Gram-negative bacteria. However, the emergence of colistin resistance, including the spread of mobile mcr genes, necessitates the development of improved diagnostics for the detection of colistin-resistant organisms in hospital settings. The recently developed MALDIxin test enables detection of colistin resistance by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) in less than 15 min but is not optimized for the mass spectrometers commonly found in clinical microbiology laboratories. In this study, we adapted the MALDIxin test for the MALDI Biotyper Sirius MALDI-TOF MS system (Bruker Daltonics). We optimized the sample preparation protocol by using a set of 6 mobile colistin resistance (MCR) protein-expressing Escherichia coli clones and validated the assay with a collection of 40 E. coli clinical isolates, including 19 confirmed MCR protein producers, 12 colistin-resistant isolates that tested negative for commonly encountered mcr genes (i.e., likely chromosomally resistant isolates), and 9 polymyxin-susceptible isolates. We calculated polymyxin resistance ratio (PRR) values from the acquired spectra; PRR values of 0, indicating polymyxin susceptibility, were obtained for all colistin-susceptible E. coli isolates, whereas positive PRR values, indicating resistance to polymyxins, were obtained for all resistant strains, independent of the genetic basis of resistance. Thus, we report a preliminary feasibility study showing that an optimized version of the MALDIxin test adapted for the routine MALDI Biotyper Sirius system provides an unbiased, fast, reliable, cost-effective, and high-throughput way of detecting colistin resistance in clinical E. coli isolates.

Coexistence Of Plasmid-Mediated mcr-1 And bla NDM-4 Genes In A Klebsiella pneumoniae Clinical Strain In Vietnam

In this study, we characterized the first clinical Klebsiella pneumoniae strain co- harboring mcr-1 and bla_NDM-4 genes in Vietnam, which was recovered from a patient admitted to hospital in 2015. This strain demonstrated nonsusceptible to all tested antibiotics, including last-line antibiotics such as carbapenems (MICs ≥128 μg/mL) and colistin (MIC =32 μg/mL), except tigecycline (MIC =1 μg/mL). Whole-genome analysis using both MinION and MiSeq data revealed that the strain carried 29 resistance genes. Particularly, mcr-1 and bla_NDM-4 genes were carried by different self-conjugative plasmids and able to be transferred to a recipient by conjugation. The colistin resistance of this strain was conferred by mcr-1 and additional chromosomal resistance determinants. Eight amino acid substitutions found in PmrA, PmrB, PmrC, PmrI, and PmrJ, all proteins that are involved in lipopolysaccharide modifications, may be associated with chromosomal colistin resistance. The accumulation of multiple antibiotic resistance mechanisms in this clinical isolate raises alarm on potential spread of extensively drug-resistant K. pneumoniae in healthcare settings.

Sequence Duplication Within pmrB Gene Contribute to High-Level Colistin Resistance in Avian Pathogenic Escherichia coli

Beyond the emergence of plasmid-encoded mechanisms, mutation within the pmrAB genes remains one of the primary colistin resistance mechanisms in Escherichia coli. However, the mechanisms of high-level colistin resistance (HLCR) have not been elucidated. In this study, we evaluated the HLCR mechanisms in five colistin-susceptible Avian pathogenic Escherichia coli (APEC) isolates after colistin exposure. Three PmrB substitutions (G19R, L167P, V88E) and two PmrB sequence duplication (PmrB-sd) mutations (68-77dup and 94-156dup) were detected. Chromosomal replacement and deletion mutagenesis revealed the two PmrB-sd mutations contribute to, but are not fully responsible for, HLCR in APEC strains. Quantitative reverse transcription/polymerase chain reaction (qRT-PCR) revealed that the PmrB-sd induction mutants showed an increased pmrAB transcript level and the PmrB-sd reversion mutants exhibited a reduction of pmrAB expression. All five induction mutants exhibited decreased minimum inhibitory concentrations to florfenicol and tetracycline. In addition, four mutants (G19R, L167P, V88E, and 94-156dup) and two mutants (68-77dup and 94-156dup) also displayed increased sensitivity to ceftiofur and gentamicin, respectively. Zeta potential measurement of the induction mutants showed that there was less negative charge on the cell surface compared with its parental strains in the absence of colistin. The induction mutants also showed an increase of lag time and decrease of fitness. In summary, the identification of novel PmrB-sd mutations contributing to HLCR is helpful to broaden the knowledge of colistin resistance. Attention should be paid to the use of colistin for the treatment of infections caused by APEC strains.

Co-occurrence of Variants of mcr-3 and mcr-8 Genes in a Klebsiella pneumoniae Isolate From Laos

Colistin is considered as a last resort antibiotic. The re-use of this antibiotic highlighted the emergence of colistin resistance mediated by chromosomal and plasmidic resistance mechanisms. Five colistin-resistant Klebsiella pneumoniae strains from Laos and Thailand were analyzed by Next Generation Sequencing (NGS) approaches to determine their colistin resistance mechanisms. Antimicrobial susceptibility testing, conjugation and transformation were performed on these strains. Moreover, whole genome sequencing (WGS) combining Illumina (MiSeq) and Oxford Nanopore technologies (MinION) was realized to obtain closed genomes and plasmids. Resistome analyses as well as location of mcr genes and its genetic environments were done in silico. All five strains had colistin MIC of 32 mg/L and were positive for mcr-3 variants including additionally positive for a mcr-8 variant gene. The novel variants were named mcr-3.21, mcr-3.26, mcr-3.28, and mcr-8.3 genes. The mcr-3 variants genes were located on plasmids IncP1, IncFII, and IncI1 type, while mcr-8.3 gene was found on an IncFII type plasmid. The genetic environment of mcr-3.21 and mcr-3.26 genes were composed of a composite transposon ISKpn40- mcr-3-dgkA- ISKpn40. Concerning mcr-8.3 gene, a similar genetic environment of mcr-8.1 gene surrounded by ISIX2 and IS903B was observed. To the best of our knowledge, this is the first description of the novel variants mcr-3.21, mcr-3.26, mcr-3.28 and mcr-8.3 genes as well as the first study on co-occurrence of mcr-3 and mcr-8 genes. Spread and evolution of mcr genes should be monitored.

Co-existence of two novel phosphoethanolamine transferase gene variants in Aeromonas jandaei from retail fish

Two novel phosphoethanolamine transferase genes, eptAv7 and eptAv3, were identified in the chromosome of an Aeromonas jandaei isolate from retail fish. The variants showed 79.9% and 80.0% amino acid identity to MCR-7.1 and MCR-3.1, respectively, and increased colistin resistance 128- to 256-fold in Aeromonas salmonicida. The two variants with no mobile genetic element in the flanking regions were also observed in other Aeromonas species. This finding supports the view that Aeromonas is a reservoir for MCR-3 and MCR-7 mobile colistin resistance.

Emergence of NDM-1- and CTX-M-3-Producing Raoultella ornithinolytica in Human Gut Microbiota

Raoultella ornithinolytica is an opportunistic pathogen of the Enterobacteriaceae family and has been implicated in nosocomial infections in recent years. The aim of this study was to characterize a carbapenemase-producing R. ornithinolytica isolate and three extended-spectrum β-lactamase (ESBL)-producing R. ornithinolytica isolates from stool samples of adults in a rural area of Shandong Province, China. The species were identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and 16S rDNA sequence analysis. Antimicrobial susceptibility test showed that all four isolates were multidrug-resistant (MDR). The whole genome sequence (WGS) of these isolates was determined using an Illumina HiSeq platform, which revealed MDR-related genes. The S1 nuclease-pulsed-field gel electrophoresis (S1-PFGE) was used to characterize the plasmids carried by the R. ornithinolytica isolates. The bla_NDM-1 and bla_CTX-M-3 genes were probed using Southern blotting, which confirmed the location of both genes on the same plasmid with molecular weight of 336.5–398.4 kb. The transferability of bla_NDM-1 and bla_CTX-M was also confirmed by conjugation assays. Finally, BLAST analysis of both genes showed that mobile genetic elements were associated with the spread of drug resistance genes. Taken together, we report the presence of conjugative bla_NDM-1 and bla_CTX-M plasmids in R. ornithinolytica isolates from healthy humans, which indicate the possibility of inter-species transfer of drug resistance genes. To the best of our knowledge, this is the first study to isolate and characterize carbapenemase-producing R. ornithinolytica and ESBL-producing R. ornithinolytica isolates from healthy human hosts.