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

Genetic framework and evolutionary dynamics of mcr-positive Klebsiella pneumoniae from 2000 to 2023

The international transmission of the colistin resistance gene mcr in Enterobacteriaceae poses significant public health burdens, while the understanding of the population structure and evolutionary history of mcr-positive Klebsiella pneumoniae worldwide remains unclear. Here, we conducted a genomic analysis on 463 sequences of K. pneumoniae harboring mcr genes from public database between 2000 and 2023. A total of 6 mcr variants (mcr-1, -2, -3, -8 to -10) were detected, with mcr-9 (36.1%), mcr-1 (33.7%) and mcr-8 (29.2%) genes being the most common. 43.4% of total isolates (201/463) carried carbapenemase genes (blaNDM, blaKPC, blaIMP, blaOXA-48/181/232, blaVIM and blaGES) and 15.3% of isolates (71/463) contained hypervirulent genes (iucA or iroB). Correlation analysis indicated mcr-1/8/9 genes were positively correlated with specific genomic elements that were rarely described, including mcr-1 with iucABC and iutA; mcr-8 with oqxB; mcr-9 with dfrA19, ISEsa and repA (R absolute value > 0.3, p<0.01). The population of K. pneumoniae can be classified into 6 clusters, some isolates co-harboring mcr and carbapenemase genes exhibited high level of genetic similarity and dispersed in several countries, indicating the possibility of clonal transmission. mcr-9 gene was introduced into K. pneumoniae in 1978 before the time of mcr-1 gene in 1988 and mcr-8 gene in 1993. We found mcr-1/8/9 genes in K. pneumoniae evolved high-risk lineages in specific geographical location (China, Thailand and the United Kingdom) that most isolates typically contained iucA, blaNDM or blaKPC. This study highlighted that continuous surveillance for the evolution of mcr-positive K. pneumoniae harboring iucA or carbapenemase genes is essential.

Emergence of mcr-8.2-mediated colistin resistance in Klebsiella pneumoniae isolated from pediatric diarrhea cases in southern Vietnam

BACKGROUND

Colistin resistance poses a growing global challenge, particularly in low- and middle-income countries where antibiotic misuse is prevalent. This study investigates the prevalence of colistin resistance in Klebsiella spp. and characterizes the genetic features of resistant isolates, focusing on the mcr-8.2 gene identified in a Klebsiella pneumoniae isolate from pediatric diarrheal cases in southern Vietnam.

METHODS

Stool samples were collected from 500 pediatric patients (aged 0-5 years) hospitalized with diarrhea in two tertiary hospitals in Ho Chi Minh City between March and September 2022. Samples were cultured on Violet Red Bile Glucose Agar, then presumptive Klebsiella spp. colonies were selected, purified on nutrient agar, and identified using MALDI-TOF MS. Colistin resistance was determined via minimum inhibitory concentration testing, and the presence of mcr genes was confirmed through polymerase chain reaction. Whole-genome sequencing was performed on the Klebsiella pneumoniae strain harboring mcr-8.2 to elucidate resistance mechanisms. Strain characterization was performed using multi-locus sequence typing, while conjugation experiments assessed horizontal gene transfer potential.

RESULTS

Among 121 Klebsiella spp. isolates, 49 (40.5%) were resistant to colistin. The mcr-1 gene was detected in 31 isolates (25.6%), whereas the mcr-8 was identified in a single isolate (0.8%), with a colistin MIC of 16 µg/mL. Genomic analysis revealed 34 antibiotic resistance genes, including mcr-8.2 and multiple β-lactamase genes, alongside plasmid types IncFIB and IncFII. Chromosomal mutations in phoP, phoQ, and lpxM were also implicated in colistin resistance.

CONCLUSIONS

This study documents the emergence of mcr-8.2-mediated colistin resistance in K. pneumoniae from pediatric diarrhea in Vietnam and highlights a high prevalence of multidrug resistance in Klebsiella spp.. Continuous surveillance of mcr genes and novel therapeutic strategies are urgently needed.

Increasing polymyxin resistance in clinical carbapenem-resistant Klebsiella pneumoniae strains in China between 2000 and 2023

BACKGROUND

Development of polymyxin resistance in carbapenem-resistant Klebsiella pneumoniae (CRKP) poses a severe challenge to public health. Here we aimed to perform a retrospective study of prevalence and molecular characteristics of polymyxin-resistant CRKP strains.

METHODS

4455 clinical CRKP strains from 18 provinces in China during 2000 to 2023 were collected. Polymyxin-resistant CRKP strains were subjected to antimicrobial susceptibility testing, whole genome sequencing and bioinformatic analysis. Molecular mechanisms underlying the polymyxin resistance in CRKP were analyzed.

RESULTS

Here we show that polymyxin-resistant CRKP emerge initially in 2014, prevalence of such strains then increase steadily over the years, reaching a rate of 9.86% in 2023. In total, 112 polymyxin-resistant CRKP isolates are identified. Antimicrobial susceptibility tests show that all polymyxin-resistant CRKP are resistant to commonly used antibiotics, yet most isolates remain susceptible only to ceftazidime-avibactam and tigecycline. Predominant polymyxin resistance mechanism in CRKP is mutations in mgrB (59/112), which commonly involves disruption of mgrB by insertion of elements such as ISKpn26 (20/59), IS903B (14/59), and ISKpn14 (9/59). Phylogenetic analysis reveals frequent clonal dissemination of polymyxin-resistant CRKP within the same hospital and even among different hospitals in neighboring provinces. pLVPK-like virulence plasmids are detected in 46 isolates, such strains are therefore categorized as polymyxin and carbapenem-resistant hypervirulent K. pneumoniae which may cause infections with high mortality.

CONCLUSIONS

Our results highlight frequent clonal transmission of polymyxin-resistant CRKP within hospitals. Continuous surveillance of polymyxin resistance among CRKP should be implemented to prevent further dissemination of such strains in clinical settings in China.

Identification of mcr-2 and mcr-3 Genes in Colistin-Resistant E. coli O157:H7 Isolated From Raw Meat Samples in Beirut, Lebanon

Colistin is a last-resort antibiotic used to treat multidrug-resistant Gram-negative bacterial infections. The global emergence of colistin resistance has been attributed to plasmid-mediated mobile colistin resistance (mcr) genes. In Lebanon, bacteria carrying the mcr-1 gene have increasingly been identified in food animal sources. This study is aimed at detecting colistin-resistant Shiga toxigenic Escherichia coli O157:H7 in raw meat samples from local markets in the suburbs of Beirut and evaluating their antimicrobial resistance profiles. A total of 50 meat samples, including 25 minced beef and 25 burger samples, were collected and analyzed. Antimicrobial resistance patterns were determined using the Kirby-Bauer method, while colistin resistance and the presence of mcr-2 and mcr-3 genes were assessed using broth microdilution and PCR amplification techniques. Among these samples, 23 (46%) tested positive for E. coli O157:H7. Resistance to ampicillin and amoxicillin/clavulanic acid was observed in 96% of the samples, while 61% were resistant to trimethoprim/sulfamethoxazole, and 43% to chloramphenicol. Notably, 87% of the samples displayed colistin resistance, with a minimum inhibitory concentration (MIC) of ≥ 4 μg/mL. The mcr-2 gene was present in four isolates (17.4%), and the mcr-3 gene was identified in 10 isolates (43.4%). This study is the first to document the presence of plasmid-mediated colistin resistance genes, mcr-2 and mcr-3, in E. coli O157:H7 strains in Lebanon. These findings highlight a serious public health concern for the Lebanese community. Therefore, the responsible use of antibiotics across all healthcare sectors, combined with strict hygiene measures in food handling, is essential to control the spread of colistin-resistant genes.

Emerging Mobile Colistin Resistance Gene Mcr-1 and Mcr-10 in Enterobacteriaceae Isolates From Urban Sewage in China

Purpose

This study aimed to investigate the epidemiology and dissemination of mcr-positive Enterobacteriaceae in urban sewage in Yangzhou, China.

Methods

A total of 366 sewage samples were collected from the Yangzhou Wastewater Treatment Plant in Jiangsu Province. Colistin-resistant Enterobacteriaceae was identified through PCR targeting mcr-1 to mcr-10 genes. The isolates underwent antimicrobial susceptibility testing, and whole-genome sequencing was performed to analyze their genomic features. Additionally, conjugation experiments were conducted to assess the transferability of mcr-positive plasmids.

Results

Three mcr-positive Enterobacteriaceae isolates were identified, representing an isolation rate of 0.82%. These included one mcr-1-positive Escherichia coli (ST167) and two mcr-10-positive Klebsiella pneumoniae complex strains with novel sequence types ST6801 and ST6825. The mcr-1 gene was located on an IncI2 plasmid (pYZ22WS208_3) and successfully transferred to recipient strains. In contrast, the mcr-10 gene was carried on IncF plasmids (pYZ22WS067_1 and pYZ22WS223_1) but was not transferable in this study. Phylogenetic analysis revealed that the mcr-1-positive E. coli strain clustered within Clade II, alongside strains from various countries and sources. Phylogenomic analysis of mcr-10-positive isolates showed their sporadic distribution across 13 countries, with associations to diverse hosts and environments, indicating potential for widespread transmission.

Conclusion

This study demonstrates the presence of mcr-1 and mcr-10-positive Enterobacteriaceae in wastewater, emphasizing the importance of wastewater surveillance for tracking antibiotic resistance. The horizontal transfer of mcr-1 and potential spread of mcr-10 across various hosts underscore the need for ongoing monitoring and preventive measures.

Emergence of mcr-8.1-bearing MDR-hypervirulent Klebsiella pneumoniae ST307

We report for the first time whole-genome sequencing of four multidrug-resistant sequence type (ST) 307 Klebsiella pneumoniae recovered from patients in two hospitals in Armenia. Comparative genomic analysis revealed that the isolates were closely related, with a maximum of 39 single nucleotide polymorphism (SNP) differences in the core genome. All Armenian isolates carried the integrative and conjugative element ICEKp4, which bears the yersiniabactin locus, and shared a common evolutionary origin, diverging around 2005 (95% CI: 1999 to 2011). Antibiotic susceptibility testing showed resistance to several antibiotics, including ampicillin, amoxicillin-clavulanic acid, cefepime, ceftazidime, norfloxacin, levofloxacin, and chloramphenicol. Specifically, isolates designated as ARM03 and ARM06 were resistant to piperacillin-tazobactam, ARM04 and ARM05 had intermediate resistance to both piperacillin-tazobactam and imipenem, and ARM03 showed intermediate resistance to amikacin. We further identified antimicrobial resistance (AMR) genes in four Armenian isolates, including blaOXA-1, blaTEM-1D, blaSHV-28, dfrA14, tet(A), sul2, qnrB1, aac(6´)-Ib-cr, strA, strB and the extended-spectrum β-lactamase gene blaCTX-M-15. Additionally, ARM03 and ARM06 also obtained dfrA5, sul1, sul3, cmlA1, mphA, aph3-Ia and the unique colistin resistance gene mcr-8.1, which was absent in all other publicly available ST307 isolates. These two isolates also acquired aerobactin siderophore-encoding gene clusters (iucABCD-iutA) and the hypermucoidy locus rmpADC (ARM06 had rmpA fragment). ARM04 and ARM05, as well as ARM03 and ARM06, had nearly identical AMR and virulence genes, along with similar plasmid replicon profiles, respectively. Our findings suggest that a transmission event occurred between the two hospitals in Armenia, likely facilitated by patients or community members, during which K. pneumoniae ST307 isolates acquired plasmids carrying AMR and virulence genes.IMPORTANCEMultidrug-resistant (MDR) Klebsiella pneumoniae sequence type (ST) 307 has emerged as a high-risk clone associated with hospital- and community-acquired infections, posing a major threat to global public health. We report in-depth comparative genomics analyses of K. pneumoniae ST307 isolates recovered from patients in Armenia. The unique colistin resistance gene mcr-8.1 identified in ARM03 and ARM06 was absent in all other ST307 isolates obtained from the publicly available data sets. ARM03 and ARM06 also acquired aerobactin siderophore-encoding gene clusters (iucABCD-iutA) and the hypermucoidy locus rmpADC (ARM06 possessed incomplete rmpA fragment). Our findings suggest that a transmission event has occurred between two hospitals in Armenia either through patients or community members. In addition, the Armenian isolates obtained plasmids carrying virulence and AMR genes during the transmission event. Our study emphasises the importance of genomic surveillance of this emerging MDR-hypervirulent pathogen to provide early interventions.

Assessment of antibiotic resistance and virulence in Escherichia coli strains isolated from poultry in Spain

Colibacillosis is a disease caused by avian pathogenic Escherichia coli (APEC) isolates which results in significant morbidity and mortality in poultry, as well as in economic loses. In order to identify APEC strains in a population of 898 E. coli isolates from poultry samples collected from different avian flocks located in the Valencian Region, Spain, we analysed the most significantly related to highly-pathogenic colibacillosis virulence-associated genes (VAGs) (hlyF, iroN, iss, iutA and ompT) by multiplex real-time polymerase chain reaction (RT-PCR). Results from this study showed that 59.5 % of the strains were identified as APEC by the expression of the five VAGs. In addition, both phenotypic and genotypic resistances to the last-resort antibiotic colistin in the same population were detected through either antimicrobial susceptibility tests or RT-PCR targeting mcr-1 and mcr-2 genes. An expected low frequency of colistin-resistant E. coli strains was detected as well as a low but noteworthy proportion of 3.3 % extremely-drug resistant strains, which encourages to still reducing the use of antibiotics in animals and humans to prevent the transmission of antimicrobial resistances among them.

Trends in CRKP Prevalence and Risk Factors for CRKP Hospital-Acquired Infections in Pediatric Patients Pre-, During-, and Post-COVID-19 Pandemic

This study aims to delineate the epidemiological trends of carbapenem-resistant Klebsiella pneumoniae (CRKP) in pediatric patients before, during, and after coronavirus disease 2019 (COVID-19) pandemic and to assess the risk factors of CRKP hospital-acquired infections (CRKP-HAIs) across these three periods. We retrospectively collected the clinical data of pediatric patients diagnosed with K. pneumoniae infection at the Children's Hospital of Nanjing Medical University from January 2018 to March 2024. Carbapenemase-related genes were detected by PCR, and statistical analysis was conducted using SPSS 25.0. The current study found that modifications in the COVID-19 pandemic prevention and control measures and antibiotic therapies impact the epidemiological trends and antimicrobial resistance of CRKP. Binary logistic regression analyses revealed various independent risk factors for CRKP-HAIs before, during, and after the COVID-19 pandemic. Healthcare institutions must intensify surveillance for HAIs, continuously monitor and avoid risk factors for CRKP-HAIs, and formulate targeted preventive and control measures to effectively reduce the incidence and spread of these infections. Further, consistent surveillance of CRKP strains coproducing carbapenemase genes is crucial for mitigating the potential health risks in pediatric patients.

Mechanisms in colistin-resistant superbugs transmissible from veterinary, livestock and animal food products to humans

In the era of antibiotic resistance, where multidrug-resistant (MDR), extensively drug resistant (XDR), and pan-drug resistant (PDR) Gram-negative infections are prevalent, it is crucial to identify the primary sources of antibiotic resistance, understand resistant mechanisms, and develop strategies to combat these mechanisms. The emergence of resistance to last-resort antibiotics like colistin has sparked a war between humanity and resistant bacteria, leaving humanity struggling to find effective countermeasures. Although colistin is used as a highly toxic antibiotic in infections that are not treated with routine antibiotics, its widespread use in animal breeding and veterinary medicine has contributed to the spread of colistin-resistant bacteria, plasmid-borne colistin resistance genes (mcr), and antibiotic residues in livestock and animal-derived foods. These sources can potentially transmit colistin resistance to humans through various routes. Therefore, managing the use of colistin in livestock and animal foods, implementing strict monitoring, and establishing guidelines for its proper use are essential to prevent the escalation of colistin resistance. This review article discusses the latest mechanisms of colistin antibiotic resistance, particularly biofilm production as a public health threat, the livestock and animal food sources of this resistance, and the routes of transmission to humans.

The multifaceted roles of phosphoethanolamine-modified lipopolysaccharides: from stress response and virulence to cationic antimicrobial resistance

SUMMARYLipopolysaccharides (LPS) are an integral part of the outer membrane of Gram-negative bacteria and play essential structural and functional roles in maintaining membrane integrity as well as in stress response and virulence. LPS comprises a membrane-anchored lipid A group, a sugar-based core region, and an O-antigen formed by repeating oligosaccharide units. 3-Deoxy-D-manno-octulosonic acid-lipid A (Kdo2-lipid A) is the minimum LPS component required for bacterial survival. While LPS modifications are not essential, they play multifaceted roles in stress response and host-pathogen interactions. Gram-negative bacteria encode several distinct LPS-modifying phosphoethanolamine transferases (PET) that add phosphoethanolamine (pEtN) to lipid A or the core region of LPS. The pet genes differ in their genomic locations, regulation mechanisms, and modification targets of the encoded enzyme, consistent with their various roles in different growth niches and under varied stress conditions. The discovery of mobile colistin resistance genes, which represent lipid A-modifying pet genes that are encoded on mobile elements and associated with resistance to the last-resort antibiotic colistin, has led to substantial interest in PETs and pEtN-modified LPS over the last decade. Here, we will review the current knowledge of the functional diversity of pEtN-based LPS modifications, including possible roles in niche-specific fitness advantages and resistance to host-produced antimicrobial peptides, and discuss how the genetic and structural diversities of PETs may impact their function. An improved understanding of the PET group will further enhance our comprehension of the stress response and virulence of Gram-negative bacteria and help contextualize host-pathogen interactions.

Two outbreak cases involving ST65-KL2 and ST11-KL64 hypervirulent carbapenem-resistant Klebsiella pneumoniae: similarity and diversity analysis

The rise of the convergence of hypervirulence and carbapenem resistance in Klebsiella pneumoniae has been increasingly reported in recent years, however, there are few outbreak cases for these producing NDM carbapenemase. In this study, ST65-KL2 and ST11-KL64 hypervirulent and carbapenem-resistant K. pneumoniae (hvCRKP) were identified from two different outbreak cases: (1) clonal spreading of ST65-KL2 in five patients within transplantation wards spanning three months; and (2) clonal transmission of ST11-KL64 in ten patients across 10 months. The representative strains of ST65-KL2 and ST11-KL64 hvCRKP, K22877 and K56649, produced carbapenemase NDM-5 and dual carbapenemases KPC-2 and NDM-13, respectively, and both exhibited high-level carbapenem resistance. Moreover, virulent analysis showed that K22877 and K56649 were hypervirulent and the former possessed stronger virulence. Evolutionary pathways suggested ST65-KL2 and ST11-KL64 hvCRKP could be classified as CR-hvKP (hvKP acquiring carbapenem resistance) and hv-CRKP (CRKP acquiring hypervirulence), respectively. Unexpectedly, ST65-KL2 CR-hvKP showed resistance to ciprofloxacin mediated by plasmid acquisition as its spread, and ST11-KL64 hv-CRKP developed into enhanced virulence and macrophage resistance. Furthermore, compared to the ST65-KL2 CR-hvKP, the ST11-KL64 hv-CRKP tends to cause occult and persistent infection. Global genome analysis revealed ST11-KL64 hv-CRKP and ST65-KL2 CR-hvKP mainly carried blaKPC-2 and had significant differences in Ompk35/36, ybt, resistance and virulence. Effective surveillance should be implemented and novel therapeutic strategies are urgently needed to deal with refractory infections.

A novel chicken-origin colistin-resistant Klebsiella pneumoniae ST5982 Co-harboring mcr-3.11 and CTX-M-27

Klebsiella pneumoniae (K. pneumoniae) is an important zoonotic opportunistic pathogen of Enterobacteriaceae that has become one of the most common infectious diseases causing Enterobacteriaceae after Escherichia coli. In this study, we identified a colistin-resistant, multidrug-resistant ST5982 K. pneumoniae strain of broiler origin. The isolate carried 35 resistance genes of 10 antibiotics classes, detected by whole genome sequencing (WGS); 11.4 % (4/35) of the resistance genes were distributed in the chromosome, and 88.6 % (31/35) of the resistance genes were located in four different resistance plasmids. Among the four plasmids, we found for the first time that CTX-M-27 and mcr-3.11 simultaneously coexisted in K. pneumoniae, and a resistance plasmid of IncI1 carrying a combination of mcr-3.11 and qnrS1 was identified. We successfully transferred mcr-3.11, qnrS1 and CTX-M-27 genes into E. coli J53 through conjugation experiments. In the present study, the co-occurrence of CTX-M-27 and mcr-3.11 in multidrug-resistant K. pneumoniae strain ST5982 was detected for the first time; its drug resistance was evaluated, and the risk of its transmission was assessed to provide a reference for further prevention and treatment of K. pneumoniae.

Whole genome analysis of multidrug-resistant Escherichia coli isolate collected from drinking water in Armenia revealed the plasmid-borne mcr-1.1-mediated colistin resistance

The rate of polymyxin-resistant Enterobacteriaceae, as well as human and animal infections caused by them, is increasing worldwide, posing a high epidemiological threat since colistin represents a last-resort antibiotic to treat complicated infections. The study of environmental niches, in particular, aquatic ecosystems in terms of genome analysis of inhabiting antimicrobial-resistant (AMR) microorganisms as reservoirs of acquired resistance determinants (AMR genes), represents a specific concern from a One Health approach. Here, we present a phenotypic AMR analysis and molecular characterization of Escherichia coli isolate found in municipal drinking water after an accident in the water supply system of a residential building in Armenia in 2021. CrieF1144 E. coli isolate was resistant to ampicillin, ampicillin/sulbactam, cefuroxime, ciprofloxacin, levofloxacin, trimethoprim/sulfamethoxazole, colistin, and tigecycline, whereas whole genome sequencing (WGS) revealed blaTEM-1B, tet(A), and a combination of dfrA14 with sul1 resistance determinants, which corresponds well with phenotypic resistance above. Moreover, the multidrug-resistant isolate studied harbored mcr-1.1 gene on a conjugative 251 Kb IncHI2 plasmid, whose structure was determined using hybrid short- and long-reads assembly. CrieF1141_p1 plasmid carried all antimicrobial resistance genes revealed in the isolate and did not harbor any virulence determinants, so it could contribute to the spread of AMR genes in the bacterial population. Two copies of ISApl1 transposase-encoding element, which is likely to mediate mcr-1.1 gene mobilization, were revealed surrounding this gene in a plasmid.

IMPORTANCE

Evolutionary patterns of Escherichia coli show that they usually develop into highly pathogenic forms by acquiring fitness advantages such as antimicrobial resistance (AMR) and various virulence factors through horizontal gene transfer mediated by mobile elements. This has led to high prevalence of multidrug-resistant (MDR) strains, which highlights the relevancy of enhanced surveillance to monitor and prevent transmission of the MDR bacteria to human and animal populations. However, the limited number of reports regarding the whole genome sequencing (WGS) investigation of MDR E. coli strains isolated from drinking water and harboring mcr genes hampers the adoption of a comprehensive approach to address the relationship between environmental E. coli populations and human and veterinary infections. Our results highlight the relevance of analyzing the environment, especially water, as a part of the surveillance programs to understand the origins and dissemination of antimicrobial resistance within the One Health concept.

Co-existence of two plasmids harboring transferable resistance-nodulation-division pump gene cluster, tmexCD1-toprJ1, and colistin resistance gene mcr-8 in Klebsiella pneumoniae

BACKGROUND

The emergence of plasmid-mediated mobile colistin resistance (mcr) gene poses a great challenge to the clinical application of polymyxins. To date, mcr-1 to mcr-10 have been found in animals, humans, and the environment. Among them, mcr-8 was first identified in Klebsiella pneumoniae (K. pneumoniae) of swine origin, and then mcr-8.1 to mcr-8.5 were successively identified. Notably, K. pneumoniae is the major host of the mcr-8 gene in both animals and humans. This study aims to explore the characteristics of K. pneumoniae strains carrying the mcr-8 gene and tmexCD1-toprJ1 gene cluster and investigate the correlation between these two antibiotic resistance genes.

METHODS

The isolates from the poultry farms and the surrounding villages were identified by mass spectrometer, and the strains positive for mcr-1 to mcr-10 were screened by polymerase chain reaction (PCR). The size of the plasmid and the antimicrobial resistance genes carried were confirmed by S1-nuclease pulsed-field gel electrophoresis (S1-PFGE) and Southern hybridization, and the transferability of the plasmid was verified by conjugation experiments. Antimicrobial susceptibility testing (AST) and whole genome sequencing (WGS) were used to characterize the strains.

RESULTS

Two K. pneumoniae isolates (KP26 and KP29) displaying polymyxin resistance were identified as mcr-8 gene carriers. Besides that, tigecycline-resistant gene cluster tmexCD1-toprJ1 was also found on the other plasmid which conferred strain resistance to tigecycline. Through epidemiological analysis, we found that the mcr-8 gene has dispersed globally, circulating in the human, animals, and the environment. Furthermore, our analysis suggests that the coexistence of mcr-8 and tmexCD1-toprJ1 on a single plasmid might evolved through plasmid recombination.

CONCLUSIONS

Although the mcr-8 and tmexCD1-toprJ1 gene clusters in the two strains of K. pneumoniae in this study were on two different plasmids, they still pose a potential threat to public health, requiring close monitoring and further study.

High-performance lung-targeted bio-responsive platform for severe colistin-resistant bacterial pneumonia therapy

Polymyxins are the last line of defense against multidrug-resistant (MDR) Gram-negative bacterial infections. However, this last resort has been threatened by the emergence of superbugs carrying the mobile colistin resistance gene-1 (mcr-1). Given the high concentration of matrix metalloproteinase 3 (MMP-3) in bacterial pneumonia, limited plasma accumulation of colistin (CST) in the lung, and potential toxicity of ionic silver (Ag+), we designed a feasible clinical transformation platform, an MMP-3 high-performance lung-targeted bio-responsive delivery system, which we named "CST&Ag@CNMS". This system exhibited excellent lung-targeting ability (>80% in lungs), MMP-3 bio-responsive release property (95% release on demand), and synergistic bactericidal activity in vitro (2-4-fold minimum inhibitory concentration reduction). In the mcr-1+ CST-resistant murine pneumonia model, treatment with CST&Ag@CNMS improved survival rates (70% vs. 20%), reduced bacteria burden (2-3 log colony-forming unit [CFU]/g tissue), and considerably mitigated inflammatory response. In this study, CST&Ag@CNMS performed better than the combination of free CST and AgNO3. We also demonstrated the superior biosafety and biodegradability of CST&Ag@CNMS both in vitro and in vivo. These findings indicate the clinical translational potential of CST&Ag@CNMS for the treatment of lung infections caused by CST-resistant bacteria carrying mcr-1.

Comparative analysis of antimicrobial resistance phenotype and genotype of Riemerella anatipestifer

Riemerella anatipestifer is one of the important bacterial pathogens that threaten the waterfowl farming industry. In this study, 157 suspected R. anatipestifer strains were isolated from diseased ducks and geese from seven regions of China during 2019-2020, and identified using multiple polymerase chain reaction (PCR). Antimicrobial susceptibility tests and whole-genome sequence (WGS) analysis were then performed for comparative analysis of antimicrobial resistance phenotypes and genotypes. The results showed that these strains were susceptible to florfenicol, ceftriaxone, spectinomycin, sulfafurazole and cefepime, but resistant to kanamycin, amikacin, gentamicin, and streptomycin, exhibiting multiple antimicrobial resistance phenotypes. WGS analysis revealed a wide distribution of genotypes among the 157 strains with no apparent regional pattern. Through next-generation sequencing analysis of antimicrobial resistance genes, a total of 88 resistance genes were identified. Of them, 19 tetracycline resistance genes were most commonly found, followed by 15 efflux pump resistance genes, 11 glycopeptide resistance genes and seven macrolide resistance genes. The 157 R. anatipestifer strains contained 42-55 resistance genes each, with the strains carrying 47 different resistance genes being the most abundant. By comparing the antimicrobial resistance phenotype and genotype, it was observed that a high correlation between them for most antimicrobial resistance properties was detected, except for a difference in aminoglycoside resistance phenotype and genotype. In conclusion, 157 R. anatipestifer strains exhibited severe multiple antimicrobial resistance phenotypes and genotypes, emphasizing the need for improved antimicrobial usage guidelines. The wide distribution and diverse types of resistance genes among these strains provide a foundation for studying novel mechanisms of antimicrobial resistance.

Repeated Occurrence of Mobile Colistin Resistance Gene-Carrying Plasmids in Pathogenic Escherichia coli from German Pig Farms

The global spread of plasmid-mediated mobile colistin resistance (mcr) genes threatens the vital role of colistin as a drug of last resort. We investigated whether the recurrent occurrence of specific E. coli pathotypes and plasmids in individual pig farms resulted from the continued presence or repeated reintroduction of distinct E. coli strains. E. coli isolates (n = 154) obtained from three pig farms with at least four consecutive years of mcr detection positive for virulence-associated genes (VAGs) predicting an intestinal pathogenic pathotype via polymerase chain reaction were analyzed. Detailed investigation of VAGs, antimicrobial resistance genes and plasmid Inc types was conducted using whole genome sequencing for 87 selected isolates. Sixty-one E. coli isolates harbored mcr-1, and one isolate carried mcr-4. On Farm 1, mcr-positive isolates were either edema disease E. coli (EDEC; 77.3%) or enterotoxigenic E. coli (ETEC; 22.7%). On Farm 2, all mcr-positive strains were ETEC, while mcr-positive isolates from Farm 3 showed a wider range of pathotypes. The mcr-1.1 gene was located on IncHI2 (Farm 1), IncX4 (Farm 2) or IncX4 and IncI2 plasmids (Farm 3). These findings suggest that various pathogenic E. coli strains play an important role in maintaining plasmid-encoded colistin resistance genes in the pig environment over time.

Epidemiology and genetic characterization of tet(X4)-positive Klebsiella pneumoniae and Klebsiella quasipneumoniae isolated from raw meat in Chengdu City, China

The rapid spread of mobile tigecycline resistance presents a significant public health threat, particularly with the increasing prevalence of tet(X4)-positive Enterobacterales across various species. This study aimed to investigate the epidemic features and transmission dynamics of tet(X4)-positive Klebsiella pneumoniae (K. pneumoniae) through the analysis of 206 raw meats, including pork (n = 182), beef (n = 16), duck (n = 5), and chicken (n = 3). These samples were collected from schools, markets, and restaurants in Chengdu City, China. A total of 25 isolates were obtained from 13 administrative regions. All isolates exhibited resistance to tetracycline, tigecycline, ampicillin, chloramphenicol, and florfenicol. Over half of the isolates also demonstrated resistance to streptomycin (80 %), sulfamethoxazole/trimethoprim (72 %), ciprofloxacin (64 %), and ampicillin/sulbactam (56 %). Among these strains, 14 distinct sequence types (STs) were identified, revealing evidence of inter-regional clonal spread, notably among 9 K. pneumoniae ST3393. Phylogenetic analysis revealed the presence of two K. pneumoniae ST5 closely resembling hypervirulent K. pneumoniae from Jiangsu. Importantly, 12 isolates were capable of transferring tigecycline resistance to Escherichia coli J53. Further plasmid analysis showed that the tet(X4)-harboring plasmids in K. pneumoniae could be classified into four types, primarily belonging to the IncFIA(HI1)/HI1A/HI1B hybrid plasmid (n = 16) and IncFII plasmid (n = 7), which significantly contributed to the cross-species dissemination of tet(X4). In summary, this study highlights the prevalence of MDR tet(X4)-positive K. pneumoniae in Chengdu, driven predominantly by clonal expansion and plasmid-mediated horizontal gene transfer. These findings emphasize the importance of continuous surveillance of tet(X4)-positive K. pneumoniae in raw meat and the implementation of effective measures to control their spread.

Plasmid-mediated colistin-resistance genes: mcr

Colistin is regarded as a last-line drug against serious infections caused by multidrug-resistant Gram-negative bacterial pathogens. Therefore, the emergence of mobile colistin resistance (mcr) genes has attracted global concern and led to policy changes for the use of colistin in food animals across many countries. Currently, the distribution, function, mechanism of action, transmission vehicles, origin of mcr, and new treatment strategies against MCR-producing pathogens have been extensively studied. Here we review the prevalence, structure and function of mcr, the fitness cost and persistence of mcr-carrying plasmids, the impact of MCR on host immune response, as well as the control strategies to combat mcr-mediated colistin resistance.

Prevalence of colistin-resistant Escherichia coli in foods and food-producing animals through the food chain: A worldwide systematic review and meta-analysis

The purpose of this systematic review and meta-analysis was to summarize the available scientific evidence on the prevalence of colistin-resistant Escherichia coli strains isolated from foods and food-producing animals, the mobile colistin-resistant genes involved, and the impact of the associated variables. A systematic review was carried out in databases according to selection criteria and search strategies established a priori. Random-effect meta-analysis models were fitted to estimate the prevalence of colistin-resistant Escherichia coli and to identify the factors associated with the outcome. In general, 4.79% (95% CI: 3.98%-5.76%) of the food and food-producing animal samples harbored colistin-resistant Escherichia coli (total number of colistin-resistant Escherichia coli/total number of samples), while 5.70% (95% confidence interval: 4.97%-6.52%) of the E. coli strains isolated from food and food-producing animal samples harbored colistin resistance (total number of colistin-resistant Escherichia coli/total number of Escherichia coli isolated samples). The prevalence of colistin-resistant Escherichia coli increased over time (P < 0.001). On the other hand, 65.30% (95% confidence interval: 57.77%-72.14%) of colistin resistance was mediated by the mobile colistin resistance-1 gene. The mobile colistin resistance-1 gene prevalence did not show increases over time (P = 0.640). According to the findings, other allelic variants (mobile colistin resistance 2-10 genes) seem to have less impact on prevalence. A higher prevalence of colistin resistance was estimated in developing countries (P < 0.001), especially in samples (feces and intestinal content, meat, and viscera) derived from poultry and pigs (P < 0.001). The mobile colistin resistance-1 gene showed a global distribution with a high prevalence in most of the regions analyzed (>50%). The prevalence of colistin-resistant Escherichia coli and the mobile colistin resistance-1 gene has a strong impact on the entire food chain. The high prevalence estimated in the retail market represents a potential risk for consumers' health. There is an urgent need to implement based-evidence risk management measures under the "One Health" approach to guarantee public health, food safety, and a sustainable future.

Co-transfer of IncFII/IncFIB and IncFII plasmids mediated by IS26 facilitates the transmission of mcr-8.1 and tmexCD1-toprJ1

PURPOSE

This study aimed to characterise the whole-genome structure of two clinical Klebsiella pneumoniae strains co-harbouring mcr-8.1 and tmexCD1-toprJ1, both resistant to colistin and tigecycline.

METHODS

K. pneumoniae strains TGC-02 (ST656) and TGC-05 (ST273) were isolated from urine samples of different patients hospitalised at separate times in 2021. Characterisation involved antimicrobial susceptibility testing (AST), conjugation assays, whole-genome sequencing (WGS), and bioinformatics analysis. Comparative genomic analysis was conducted on mcr-8.1-carrying and tmexCD1-toprJ1-carrying plasmids.

RESULTS

Both K. pneumoniae isolates displayed a multidrug-resistant phenotype, exhibiting resistance or reduced susceptibility to ampicillin, ampicillin/sulbactam, cefazolin, aztreonam, amikacin, gentamicin, tobramycin, ciprofloxacin, levofloxacin, nitrofurantoin, trimethoprim/sulfamethoxazole, apramycin, tigecycline and colistin. WGS analysis revealed that clinical strain TGC-02 carried the TmexCD1-toprJ1 gene on a 200-Kb IncFII/IncFIB-type plasmid, while mcr-8 was situated on a 146-Kb IncFII-type plasmid. In clinical strain TGC-05, TmexCD1-toprJ1 was found on a 300-Kb IncFIB/IncHI1B/IncR-type plasmid, and mcr-8 was identified on a 137-Kb IncFII/IncFIA-type plasmid. Conjugation experiments assessed the transferability of these plasmids. While transconjugants were not obtained for TGC-05 despite multiple screening with tigecycline or colistin, pTGC-02-tmex and pTGC-02-mcr8 from clinical K. pneumoniae TGC-02 demonstrated self-transferability through conjugation. Notably, the rearrangement of pTGC-02-tmex and pTGC-02-mcr8 via IS26-based homologous recombination was observed. Moreover, the conjugative and fusion plasmids of the transconjugant co-harboured the tmexCD1-toprJ1 gene cluster and mcr-8.1, potentially resulting from IS26-based homologous recombination.

CONCLUSION

The emergence of colistin- and tigecycline-resistant K. pneumoniae strains is concerning, and effective surveillance measures should be implemented to prevent further dissemination.

Stenotrophomonas riyadhensis sp. nov., isolated from a hospital floor swab

During the analysis of a collection of Pseudomonas strains linked to an outbreak in an intensive care unit at King Faisal Specialist Hospital and Research Center in 2019, one isolate (CFS3442T) was identified phenotypically as Pseudomonas aeruginosa. However, whole-genome sequencing revealed its true identity as a member of the genus Stenotrophomonas, distinct from both P. aeruginosa and Stenotrophomonas maltophilia. The isolate demonstrated: (i) a significant phylogenetic distance from P. aeruginosa; (ii) considerable genomic differences from several S. maltophilia reference strains and other Stenotrophomonas species; and (iii) unique phenotypic characteristics. Based on the combined geno- and phenotypic data, we propose that this isolate represents a novel species within the genus Stenotrophomonas, for which the name Stenotrophomonas riyadhensis sp. nov. is proposed. The type strain is CFS3442T (=NCTC 14921T=LMG 33162T).

Blanket antimicrobial resistance gene database with structural information, BOARDS, provides insights on historical landscape of resistance prevalence and effects of mutations in enzyme structure

Antimicrobial resistance (AMR) in pathogenic bacteria poses a significant threat to public health, yet there is still a need for development in the tools to deeply understand AMR genes based on genetic or structural information. In this study, we present an interactive web database named Blanket Overarching Antimicrobial-Resistance gene Database with Structural information (BOARDS, sbml.unist.ac.kr), a database that comprehensively includes 3,943 reported AMR gene information for 1,997 extended spectrum beta-lactamase (ESBL) and 1,946 other genes as well as a total of 27,395 predicted protein structures. These structures, which include both wild-type AMR genes and their mutants, were derived from 80,094 publicly available whole-genome sequences. In addition, we developed the rapid analysis and detection tool of antimicrobial-resistance (RADAR), a one-stop analysis pipeline to detect AMR genes across whole-genome sequencing (WGSs). By integrating BOARDS and RADAR, the AMR prevalence landscape for eight multi-drug resistant pathogens was reconstructed, leading to unexpected findings such as the pre-existence of the MCR genes before their official reports. Enzymatic structure prediction-based analysis revealed that the occurrence of mutations found in some ESBL genes was found to be closely related to the binding affinities with their antibiotic substrates. Overall, BOARDS can play a significant role in performing in-depth analysis on AMR.IMPORTANCEWhile the increasing antibiotic resistance (AMR) in pathogen has been a burden on public health, effective tools for deep understanding of AMR based on genetic or structural information remain limited. In this study, a blanket overarching antimicrobial-resistance gene database with structure information (BOARDS)-a web-based database that comprehensively collected AMR gene data with predictive protein structural information was constructed. Additionally, we report the development of a RADAR pipeline that can analyze whole-genome sequences as well. BOARDS, which includes sequence and structural information, has shown the historical landscape and prevalence of the AMR genes and can provide insight into single-nucleotide polymorphism effects on antibiotic degrading enzymes within protein structures.

Adult zebrafish infected by clinically isolated Klebsiella pneumoniae with different virulence showed increased intestinal inflammation and disturbed intestinal microbial biodiversity

BACKGROUND

Klebsiella pneumoniae is a pathogen that often infects patients in clinical practice. Due to its high virulent and drug resistance, infected patients are difficult to treat. In clinical practice, Klebsiella pneumoniae can infect patients' intestines, intestines, blood, etc., causing pathological changes. However, there is relatively little information on the impact of Klebsiella pneumoniae on intestinal inflammation and microbial populations. Zebrafish is an excellent biomedical model that has been successfully applied to the virulence assessment of Klebsiella pneumoniae.

METHODS

In this study, three clinically isolated representative strains of Klebsiella pneumoniae (high virulence non-resistant, high virulence resistant, and low virulence resistant) were used to infect zebrafish, and their effects on intestinal colonization, inflammation, pathology, and microbial diversity were tested.

RESULTS

Enzyme-linked immunoassay (ELISA) showed that Klebsiella pneumoniae significantly increased levels of the cytokines interleukin-1α (Il-1α), interleukin-1β (Il-1β), and tumor necrosis factor-α (Tnf-α), which increased inflammatory symptoms. Hematoxylin eosin staining(H&S) showed that Klebsiella pneumoniae treatment caused intestinal lesions in zebrafish, in which KP1053 exposure significantly decreased the number of goblet cells, KP1195 caused epithelial dissolution and exfoliation. In addition, Klebsiella pneumoniae disturbed the composition of intestinal microbiota, and the Shannon index increased, which increased the number of harmful bacteria.

CONCLUSIONS

Klebsiella pneumoniae infection can lead to intestinal colonization, inflammation, pathological changes, and changes in microbial biodiversity. This study provides a reference for the intestinal pathology of clinical Klebsiella pneumoniae infection.

Emergence of colistin-resistant Enterobacter cloacae and Raoultella ornithinolytica carrying the phosphoethanolamine transferase gene, mcr-9, derived from vegetables in Japan

IMPORTANCE

Plasmid-mediated mobile colistin-resistance genes have been recognized as a global threat because they jeopardize the efficacy of colistin in therapeutic practice. Here, we described the genetic features of two mcr-9.1-carrying Gram-negative bacteria with a colistin-resistant phenotype derived from vegetables in Japan. The colistin-resistant mcr-9.1, which has never been detected in vegetables, was located on a large plasmid in Enterobacter cloacae CST17-2 and Raoultella ornithinolytica CST129-1, suggesting a high chance of horizontal gene transfer. To the best of our knowledge, this is the first report of mcr-9 in R. ornithinolytica. This study indicates that fresh vegetables might be a potential source for the transmission of mcr-9 genes encoding resistance to frontline (colistin) and clinically relevant antimicrobials. The study also provides additional consideration for colistin use and the relevance of routine surveillance in epidemiological perspective to curb the continuous spread of mcr alleles.

Phenotypic and genotypic characterization of colistin-resistant Escherichia Coli with mcr-4, mcr-5, mcr-6, and mcr-9 genes from broiler chicken and farm environment

BACKGROUND

Colistin is an antibiotic used as a last-resort to treat multidrug-resistant Gram-negative bacterial infections. Colistin had been used for a long time in veterinary medicine for disease control and as a growth promoter in food-producing animals. This excessive use of colistin in food animals causes an increase in colistin resistance. This study aimed to determine molecular characteristics of colistin-resistant Escherichia coli in broiler chicken and chicken farm environments.

RESULTS

Four hundred fifty-three cloacal and farm environment samples were collected from six different commercial chicken farms in Kelantan, Malaysia. E. coli was isolated using standard bacteriological methods, and the isolates were tested for antimicrobial susceptibility using disc diffusion and colistin minimum inhibitory concentration (MIC) by broth microdilution. Multiplex PCR was used to detect mcr genes, and DNA sequencing was used to confirm the resistance genes. Virulence gene detection, phylogroup, and multilocus sequence typing (MLST) were done to further characterize the E. coli isolates. Out of the 425 (94%; 425/453) E. coli isolated from the chicken and farm environment samples, 10.8% (48/425) isolates were carrying one or more colistin-resistance encoding genes. Of the 48 colistin-resistant isolates, 54.2% (26/48) of the mcr positive isolates were genotypically and phenotypically resistant to colistin with MIC of colistin ≥ 4 μg/ml. The most prominent mcr gene detected was mcr-1 (47.9%; 23/48), followed by mcr-8 (18.8%; 9/48), mcr-7 (14.5%; 7/48), mcr-6 (12.5%; 6/48), mcr-4 (2.1%; 1/48), mcr-5 (2.1%; 1/48), and mcr-9 (2.1%; 1/48) genes. One E. coli isolate originating from the fecal sample was found to harbor both mcr-4 and mcr-6 genes and another isolate from the drinking water sample was carrying mcr-1 and mcr-8 genes. The majority of the mcr positive isolates were categorized under phylogroup A followed by phylogroup B1. The most prevalent sequence typing (ST) was ST1771 (n = 4) followed by ST206 (n = 3). 100% of the mcr positive E. coli isolates were multidrug resistant. The most frequently detected virulence genes among mcr positive E. coli isolates were ast (38%; 18/48) followed by iss (23%; 11/48). This is the first research to report the prevalence of mcr-4, mcr-5, mcr-6, mcr-7, and mcr-8 genes in E. coli from broiler chickens and farm environments in Malaysia.

CONCLUSION

Our findings suggest that broiler chickens and broiler farm environments could be reservoirs of colistin-resistant E. coli, posing a risk to public health and food safety.

The dynamic evolution and IS26-mediated interspecies transfer of a blaNDM-1-bearing fusion plasmid leading to a hypervirulent carbapenem-resistant Klebsiella pneumoniae strain harbouring blaKPC-2 in a single patient

OBJECTIVES

To characterize the evolution and interspecies transfer of plasmids between Klebsiella pneumoniae and Escherichia coli within a single patient.

METHODS

Minimum inhibitory concentrations were measured using broth microdilution assays. Conjugation assays, string tests, and Galleria mellonella infection model experiments were also conducted. Whole-genome sequencing was performed on the Illumina and Nanopore platforms. Antimicrobial resistance determinants, insertion sequences, and virulence factors were identified using ABRicate/ResFinder database, ISFinder, and virulence factor database. Wzi and capsular polysaccharide (KL) were typed using Kleborate and Kaptive. Multi-locus sequence typing (MLST), replicon typing, and single nucleotide polymorphism analyses were conducted using the BacWGSTdb server.

RESULTS

The carbapenem-resistant K. pneumoniae 2111KP was characterized as ST11, wzi64, and KL64, with a positive string test result and a relatively high virulence phenotype. Analysis of the 2111KP genome revealed that blaNDM-1 was located in a 268,400-bp IncFIB/IncHI1B/IncX3 conjugative plasmid (p2111KP-1), regulated by IS26, IS5, and ISKox3. p2111KP-1 was also a rmpA2-associated virulence plasmid with an iutA-iucABCD gene cluster and a IS26-mediated multidrug-resistant fusion plasmid, which contained 8-bp (AGCTGCAC or GGCCTTTG) target site duplications. Segments flanked by IS26 of p2111KP-1 were 99.99% identical to a 49,016-bp E. coli plasmid.

CONCLUSIONS

This study provided direct evidence of plasmid fusion via IS26 between two different bacterial species within one patient and revealed the process by which genetic elements conferring carbapenem resistance and virulence were simultaneously transferred between these species. It highlights the need for strategic antibiotic use and rigorous monitoring to prevent the plasmid-mediated fusion and transmission of drug-resistance/virulence factors.

A Review of Resistance to Polymyxins and Evolving Mobile Colistin Resistance Gene (mcr) among Pathogens of Clinical Significance

The global rise in antibiotic resistance in bacteria poses a major challenge in treating infectious diseases. Polymyxins (e.g., polymyxin B and colistin) are last-resort antibiotics against resistant Gram-negative bacteria, but the effectiveness of polymyxins is decreasing due to widespread resistance among clinical isolates. The aim of this literature review was to decipher the evolving mechanisms of resistance to polymyxins among pathogens of clinical significance. We deciphered the molecular determinants of polymyxin resistance, including distinct intrinsic molecular pathways of resistance as well as evolutionary characteristics of mobile colistin resistance. Among clinical isolates, Acinetobacter stains represent a diversified evolution of resistance, with distinct molecular mechanisms of intrinsic resistance including naxD, lpxACD, and stkR gene deletion. On the other hand, Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa are usually resistant via the PhoP-PhoQ and PmrA-PmrB pathways. Molecular evolutionary analysis of mcr genes was undertaken to show relative relatedness across the ten main lineages. Understanding the molecular determinants of resistance to polymyxins may help develop suitable and effective methods for detecting polymyxin resistance determinants and the development of novel antimicrobial molecules.

Combatting resistance: Understanding multi-drug resistant pathogens in intensive care units

The escalating misuse and excessive utilization of antibiotics have led to the widespread dissemination of drug-resistant bacteria, posing a significant global healthcare crisis. Of particular concern is the increasing prevalence of multi-drug resistant (MDR) opportunistic pathogens in Intensive Care Units (ICUs), which presents a severe threat to public health and contributes to substantial morbidity and mortality. Among them, MDR ESKAPE pathogens account for the vast majority of these opportunistic pathogens. This comprehensive review provides a meticulous analysis of the current prevalence landscape of MDR opportunistic pathogens in ICUs, especially in ESKAPE pathogens, illuminating their resistance mechanisms against commonly employed first-line antibiotics, including polymyxins, carbapenems, and tigecycline. Furthermore, this review explores innovative strategies aimed at preventing and controlling the emergence and spread of resistance. By emphasizing the urgent need for robust measures to combat nosocomial infections caused by MDR opportunistic pathogens in ICUs, this study serves as an invaluable reference for future investigations in the field of antibiotic resistance.

Large-scale genomic survey and characterization of mcr genes carried by foodborne Cronobacter isolates

IMPORTANCE

Cronobacter is an emerging foodborne opportunistic pathogen, which can cause neonatal meningitis, bacteremia, and NEC by contaminating food. However, the entire picture of foodborne Cronobacter carriage of the mcr genes is not known. Here, we investigated the mcr genes of Cronobacter isolates by whole-genome sequencing and found 133 previously undescribed Cronobacter isolates carrying mcr genes. Further genomic analysis revealed that these mcr genes mainly belonged to the mcr-9 and mcr-10. Genomic analysis of the flanking structures of mcr genes revealed that two core flanking structures were prevalent in foodborne Cronobacter isolates, and the flanking structure carrying IS1R was found for the first time in this study.

First Report and Characterization of the mcr-1 Positive Multidrug-Resistant Escherichia coli Strain Isolated from Pigs in Croatia

The emergence and rapid spread of the plasmid-mediated colistin-resistant mcr-1 gene introduced a serious threat to public health. In 2021, a multi-drug resistant, mcr-1 positive Escherichia coli EC1945 strain, was isolated from pig caecal content in Croatia. Antimicrobial susceptibility testing and whole genome sequencing were performed. Bioinformatics tools were used to determine the presence of resistance genes, plasmid Inc groups, serotype, sequence type, virulence factors, and plasmid reconstruction. The isolated strain showed phenotypic and genotypic resistance to nine antimicrobial classes. It was resistant to colistin, gentamicin, ampicillin, cefepime, cefotaxime, ceftazidime, sulfamethoxazole, chloramphenicol, nalidixic acid, and ciprofloxacin. Antimicrobial resistance genes included mcr-1, blaTEM-1B, blaCTX-M-1, aac(3)-IId, aph(3')-Ia, aadA5, sul2, catA1, gyrA (S83L, D87N), and parC (A56T, S80I). The mcr-1 gene was located within the conjugative IncX4 plasmid. IncI1, IncFIB, and IncFII plasmids were also detected. The isolate also harbored 14 virulence genes and was classified as ST744 and O101:H10. ST744 is a member of the ST10 group which includes commensal, extraintestinal pathogenic E. coli isolates that play a crucial role as a reservoir of genes. Further efforts are needed to identify mcr-1-carrying E. coli isolates in Croatia, especially in food-producing animals to identify such gene reservoirs.

Untying the anchor for the lipopolysaccharide: lipid A structural modification systems offer diagnostic and therapeutic options to tackle polymyxin resistance

Polymyxin antibiotics are the last resort for treating patients in intensive care units infected with multiple-resistant Gram-negative bacteria. Due to their polycationic structure, their mode of action is based on an ionic interaction with the negatively charged lipid A portion of the lipopolysaccharide (LPS). The most prevalent polymyxin resistance mechanisms involve covalent modifications of lipid A: addition of the cationic sugar 4-amino-L-arabinose (L-Ara4N) and/or phosphoethanolamine (pEtN). The modified structure of lipid A has a lower net negative charge, leading to the repulsion of polymyxins and bacterial resistance to membrane disruption. Genes encoding the enzymatic systems involved in these modifications can be transferred either through chromosomes or mobile genetic elements. Therefore, new approaches to resistance diagnostics have been developed. On another note, interfering with these enzymatic systems might offer new therapeutic targets for drug discovery. This literature review focuses on diagnostic approaches based on structural changes in lipid A and on the therapeutic potential of molecules interfering with these changes.

Emergence of novel tigecycline resistance gene tet(X5) variant in multidrug-resistant Acinetobacter indicus of swine farming environments

Antibiotic-resistant bacteria are emerging all the time, but the continued emergence of novel resistance genes and genetic structures is even more alarming. Tigecycline is currently the important last barrier in the treatment of multidrug-resistant (MDR) infections. tet(X), a resistance gene to tigecycline, is the most prevalent and constantly emerging novel variants. In this research, we characterized two MDR Acinetobacter indicus strains to tigecycline that were identified and analyzed by antimicrobial susceptibility testing, conjugation transfer, whole genome sequencing (WGS) and bioinformatics analysis, and gene function analysis. The results showed that three tet(X) variants were carried in BDT201, including tet(X6) on the chromosome, tet(X3) on the plasmid pBDT201-2, and a novel tet(X5) variant adjacent to the ISAba1 elements on the plasmid pBDT201-3. The novel Tet(X5) variant showed 98.7% amino acid identity with Tet(X5) and was named Tet(X5.4). By expressing tet(X5.4) gene, the tigecycline minimum inhibitory concentration (MIC) values for Escherichia coli JM109 increased 32- fold (from 0.13 to 4 mg/L). BDT2076 contained tigecycline and carbapenems resistance genes, such as tet(X3), blaOXA-58, blaNDM-3, and blaCARB-2. The continuous emergence of MDR bacteria and resistance genes is a global environmental health issue that can not be ignored and therefore needs to pay more urgent attention to it.

Phosphoethanolamine Transferases as Drug Discovery Targets for Therapeutic Treatment of Multi-Drug Resistant Pathogenic Gram-Negative Bacteria

Antibiotic resistance caused by multidrug-resistant (MDR) bacteria is a major challenge to global public health. Polymyxins are increasingly being used as last-in-line antibiotics to treat MDR Gram-negative bacterial infections, but resistance development renders them ineffective for empirical therapy. The main mechanism that bacteria use to defend against polymyxins is to modify the lipid A headgroups of the outer membrane by adding phosphoethanolamine (PEA) moieties. In addition to lipid A modifying PEA transferases, Gram-negative bacteria possess PEA transferases that decorate proteins and glycans. This review provides a comprehensive overview of the function, structure, and mechanism of action of PEA transferases identified in pathogenic Gram-negative bacteria. It also summarizes the current drug development progress targeting this enzyme family, which could reverse antibiotic resistance to polymyxins to restore their utility in empiric therapy.

Characteristics and genomic epidemiology of colistin-resistant Enterobacterales from farmers, swine, and hospitalized patients in Thailand, 2014-2017

BACKGROUND

Colistin is one of the last resort therapeutic options for treating carbapenemase-producing Enterobacterales, which are resistant to a broad range of beta-lactam antibiotics. However, the increased use of colistin in clinical and livestock farming settings in Thailand and China, has led to the inevitable emergence of colistin resistance. To better understand the rise of colistin-resistant strains in each of these settings, we characterized colistin-resistant Enterobacterales isolated from farmers, swine, and hospitalized patients in Thailand.

METHODS

Enterobacterales were isolated from 149 stool samples or rectal swabs collected from farmers, pigs, and hospitalized patients in Thailand between November 2014-December 2017. Confirmed colistin-resistant isolates were sequenced. Genomic analyses included species identification, multilocus sequence typing, and detection of antimicrobial resistance determinants and plasmids.

RESULTS

The overall colistin-resistant Enterobacterales colonization rate was 26.2% (n = 39/149). The plasmid-mediated colistin-resistance gene (mcr) was detected in all 25 Escherichia coli isolates and 9 of 14 (64.3%) Klebsiella spp. isolates. Five novel mcr allelic variants were also identified: mcr-2.3, mcr-3.21, mcr-3.22, mcr-3.23, and mcr-3.24, that were only detected in E. coli and Klebsiella spp. isolates from farmed pigs.

CONCLUSION

Our data confirmed the presence of colistin-resistance genes in combination with extended spectrum beta-lactamase genes in bacterial isolates from farmers, swine, and patients in Thailand. Differences between the colistin-resistance mechanisms of Escherichia coli and Klebsiella pneumoniae in hospitalized patients were observed, as expected. Additionally, we identified mobile colistin-resistance mcr-1.1 genes from swine and patient isolates belonging to plasmids of the same incompatibility group. This supported the possibility that horizontal transmission of bacterial strains or plasmid-mediated colistin-resistance genes occurs between humans and swine.

Cross-species transmission and PB2 mammalian adaptations of highly pathogenic avian influenza A/H5N1 viruses in Chile

H5N1 highly pathogenic avian influenza viruses (HPAIV) emerged in wild birds in Chile in December 2022 and spilled over into poultry, marine mammals, and one human. Between December 9, 2022 - March 14, 2023, a coordinated government/academic response detected HPAIV by real-time RT-PCR in 8.5% (412/4735) of samples from 23 avian and 3 mammal orders. Whole-genome sequences obtained from 77 birds and 8 marine mammals revealed that all Chilean H5N1 viruses belong to lineage 2.3.4.4b and cluster monophyletically with viruses from Peru, indicating a single introduction from North America into Peru/Chile. Mammalian adaptations were identified in the PB2 segment: D701N in two sea lions, one human, and one shorebird, and Q591K in the human and one sea lion. Minor variant analysis revealed that D701N was present in 52.9 - 70.9% of sequence reads, indicating the presence of both genotypes within hosts. Further surveillance of spillover events is warranted to assess the emergence and potential onward transmission of mammalian adapted H5N1 HPAIV in South America.

Prevalence and molecular characterization of mcr-1-positive foodborne ST34-Salmonella isolates in China

Salmonella enterica serovar Typhimurium (S. Typhimurium) and S. 4,[5],12:i:- have become the most common serovars associated with human salmonellosis worldwide. Moreover, the emergence of mcr-carrying S. Typhimurium and S. 4,[5],12:i:- with multidrug resistance (MDR) patterns has posed a threat to public health. In this study, we retrospectively screened 2009-2022 laboratory-preserved strains for the presence of mcr genes. We obtained 16 mcr-1-positive S. Typhimurium and S. 4,[5],12:i:- strains with MDR that belonged to sequence type 34 (ST34). Whole-genome sequencing analysis revealed that the mcr-1 was located on the IncI2 or IncHI2 plasmids. The ISApl1 element downstream of mcr-1 was present in all pig-derived strains. Conjugation experiments confirmed that nine mcr-1-carrying IncHI2 plasmids could not be transferred to Escherichia coli due to loss of the conjugation region. Finally, core genome single nucleotide polymorphism (cgSNP) analyses of the 16 mcr-1-carrying strains and 77 mcr-carrying ST34-Salmonella genome sequences from the NCBI and ENA databases showed that five out of eight clusters contained strains from pig and pig products, revealing pigs and pig products as key reservoirs of mcr-1-positive ST34-Salmonella strains. The transmission of mcr-carrying ST34 Salmonella strains to humans via the pig food chain is a potential cause for public health concern in controlling human salmonellosis.

Escherichia coli B-Strains Are Intrinsically Resistant to Colistin and Not Suitable for Characterization and Identification of mcr Genes

Antimicrobial resistance is an increasing threat to human and animal health. Due to the rise of multi-, extensive, and pandrug resistance, last resort antibiotics, such as colistin, are extremely important in human medicine. While the distribution of colistin resistance genes can be tracked through sequencing methods, phenotypic characterization of putative antimicrobial resistance (AMR) genes is still important to confirm the phenotype conferred by different genes. While heterologous expression of AMR genes (e.g., in Escherichia coli) is a common approach, so far, no standard methods for heterologous expression and characterization of mcr genes exist. E. coli B-strains, designed for optimum protein expression, are frequently utilized. Here, we report that four E. coli B-strains are intrinsically resistant to colistin (MIC 8-16 μg/mL). The three tested B-strains that encode T7 RNA polymerase show growth defects when transformed with empty or mcr-expressing pET17b plasmids and grown in the presence of IPTG; K-12 or B-strains without T7 RNA polymerase do not show these growth defects. E. coli SHuffle T7 express carrying empty pET17b also skips wells in colistin MIC assays in the presence of IPTG. These phenotypes could explain why B-strains were erroneously reported as colistin susceptible. Analysis of existing genome data identified one nonsynonymous change in each pmrA and pmrB in all four E. coli B-strains; the E121K change in PmrB has previously been linked to intrinsic colistin resistance. We conclude that E. coli B-strains are not appropriate heterologous expression hosts for identification and characterization of mcr genes. IMPORTANCE Given the rise in multidrug, extensive drug, and pandrug resistance in bacteria and the increasing use of colistin to treat human infections, occurrence of mcr genes threatens human health, and characterization of these resistance genes becomes more important. We show that three commonly used heterologous expression strains are intrinsically resistant to colistin. This is important because these strains have previously been used to characterize and identify new mobile colistin resistance (mcr) genes. We also show that expression plasmids (i.e., pET17b) without inserts cause cell viability defects when carried by B-strains with T7 RNA polymerase and grown in the presence of IPTG. Our findings are important as they will facilitate improved selection of heterologous strains and plasmid combinations for characterizing AMR genes, which will be particularly important with a shift to Culture-independent diagnostic tests where bacterial isolates become increasingly less available for characterization.

Oxazolidinone resistance genes in florfenicol-resistant enterococci from beef cattle and veal calves at slaughter

Background

Linezolid is a critically important oxazolidinone antibiotic used in human medicine. Although linezolid is not licensed for use in food-producing animals, the use of florfenicol in veterinary medicine co-selects for oxazolidinone resistance genes.

Objective

This study aimed to assess the occurrence of cfr, optrA, and poxtA in florfenicol-resistant isolates from beef cattle and veal calves from different herds in Switzerland.

Methods

A total of 618 cecal samples taken from beef cattle and veal calves at slaughter originating from 199 herds were cultured after an enrichment step on a selective medium containing 10 mg/L florfenicol. Isolates were screened by PCR for cfr, optrA, and poxtA which are genes known to confer resistance to oxazolidinones and phenicols. One isolate per PCR-positive species and herd was selected for antimicrobial susceptibility testing (AST) and whole-genome sequencing (WGS).

Results

Overall, 105 florfenicol-resistant isolates were obtained from 99 (16%) of the samples, corresponding to 4% of the beef cattle herds and 24% of the veal calf herds. Screening by PCR revealed the presence of optrA in 95 (90%) and poxtA in 22 (21%) of the isolates. None of the isolates contained cfr. Isolates included for AST and WGS analysis were Enterococcus (E.) faecalis (n = 14), E. faecium (n = 12), E. dispar (n = 1), E. durans (n = 2), E. gallinarum (n = 1), Vagococcus (V.) lutrae (n = 2), Aerococcus (A.) urinaeequi (n = 1), and Companilactobacillus (C.) farciminis (n = 1). Thirteen isolates exhibited phenotypic linezolid resistance. Three novel OptrA variants were identified. Multilocus sequence typing identified four E. faecium ST18 belonging to hospital-associated clade A1. There was a difference in the replicon profile among optrA- and poxtA-harboring plasmids, with rep9 (RepA_N) plasmids dominating in optrA-harboring E. faecalis and rep2 (Inc18) and rep29 (Rep_3) plasmids in poxtA-carrying E. faecium.

Conclusion

Beef cattle and veal calves are reservoirs for enterococci with acquired linezolid resistance genes optrA and poxtA. The presence of E. faecium ST18 highlights the zoonotic potential of some bovine isolates. The dispersal of clinically relevant oxazolidinone resistance genes throughout a wide variety of species including Enterococcus spp., V. lutrae, A. urinaeequi, and the probiotic C. farciminis in food-producing animals is a public health concern.

More than mcr: canonical plasmid- and transposon-encoded mobilized colistin resistance genes represent a subset of phosphoethanolamine transferases

Mobilized colistin resistance genes (mcr) may confer resistance to the last-resort antimicrobial colistin and can often be transmitted horizontally. mcr encode phosphoethanolamine transferases (PET), which are closely related to chromosomally encoded, intrinsic lipid modification PET (i-PET; e.g., EptA, EptB, CptA). To gain insight into the evolution of mcr within the context of i-PET, we identified 69,814 MCR-like proteins present across 256 bacterial genera (obtained by querying known MCR family representatives against the National Center for Biotechnology Information [NCBI] non-redundant protein database via protein BLAST). We subsequently identified 125 putative novel mcr-like genes, which were located on the same contig as (i) ≥1 plasmid replicon and (ii) ≥1 additional antimicrobial resistance gene (obtained by querying the PlasmidFinder database and NCBI's National Database of Antibiotic Resistant Organisms, respectively, via nucleotide BLAST). At 80% amino acid identity, these putative novel MCR-like proteins formed 13 clusters, five of which represented putative novel MCR families. Sequence similarity and a maximum likelihood phylogeny of mcr, putative novel mcr-like, and ipet genes indicated that sequence similarity was insufficient to discriminate mcr from ipet genes. A mixed-effect model of evolution (MEME) indicated that site- and branch-specific positive selection played a role in the evolution of alleles within the mcr-2 and mcr-9 families. MEME suggested that positive selection played a role in the diversification of several residues in structurally important regions, including (i) a bridging region that connects the membrane-bound and catalytic periplasmic domains, and (ii) a periplasmic loop juxtaposing the substrate entry tunnel. Moreover, eptA and mcr were localized within different genomic contexts. Canonical eptA genes were typically chromosomally encoded in an operon with a two-component regulatory system or adjacent to a TetR-type regulator. Conversely, mcr were represented by single-gene operons or adjacent to pap2 and dgkA, which encode a PAP2 family lipid A phosphatase and diacylglycerol kinase, respectively. Our data suggest that eptA can give rise to "colistin resistance genes" through various mechanisms, including mobilization, selection, and diversification of genomic context and regulatory pathways. These mechanisms likely altered gene expression levels and enzyme activity, allowing bona fide eptA to evolve to function in colistin resistance.

The First Report of Escherichia coli and Klebsiella pneumoniae Strains That Produce Both NDM-5 and OXA-181 in Jiangsu Province, China

Objective

The aim of this study was to analyze the genetic characteristics of three Enterobacteriaceae strains (one strain of Escherichia coli and two strains of Klebsiella pneumoniae) that produce both the NDM-5 and OXA-181 carbapenemases in pediatric patients.

Methods

Carbapenem-resistant Enterobacteriaceae (CRE) strains were collected from the Children's Hospital Affiliated to Nanjing Medical University in 2022. Resistance genes were detected by PCR. CRE strains that produced both the bla_NDM-5 and bla_OXA-181 genes were further characterized by antimicrobial susceptibility testing, multilocus sequence typing (MLST), plasmid conjugation assay, S1 nuclease-PFGE, Southern blotting and whole-genome sequencing.

Results

Three Enterobacteriaceae strains carrying both the bla_NDM-5 and bla_OXA-181 resistance genes were screened. MLST results showed that the strain of Escherichia coli carrying both bla_NDM-5 and bla_OXA-181 was ST410; the two strains of Klebsiella pneumoniae with both bla_NDM-5 and bla_OXA-181 were ST2601 and ST759. Conjugation assays showed that the plasmids harboring the bla_NDM-5 and bla_OXA-181 genes were self-transmissible. S1-PFGE and Southern blotting showed that the bla_NDM-5 and bla_OXA-181 genes were located on the plasmid with the size of about 60kb~. The genotyping results showed that the plasmid types were ColKP3 and IncX3.

Conclusion

This is the first report of Enterobacteriaceae strains that produce both NDM-5 and OXA-181 isolated from pediatric patients in China. Active infection control measures are urgently needed to prevent the spread of bacteria in children.

Characterization of two novel colistin resistance gene mcr-1 variants originated from Moraxella spp

This study aimed to characterize two novel mcr-1 variants, mcr-1.35 and mcr-1.36, which originated from Moraxella spp. that were isolated from diseased pigs in China. The Moraxella spp. carrying novel mcr-1 variants were subjected to whole-genome sequencing (WGS) and phylogenetic analysis based on the 16S rRNA gene. The mcr-1 variants mcr-1.35 and mcr-1.36 were characterized using phylogenetic analysis, a comparison of genetic environments, and protein structure prediction. The WGS indicated that two novel mcr-1 variants were located in the chromosomes of three Moraxella spp. with a genetic environment of mcr-1-pap2. In addition to the novel colistin resistance genes mcr-1.35 and mcr-1.36, the three Moraxella spp. contained other antimicrobial resistance genes, including aac(3)-IId, tet(O), sul2, floR, and bla_ROB-3. A functional cloning assay indicated that either the mcr-1.35 or mcr-1.36 gene could confer resistance to colistin in Escherichia coli DH5α and JM109. The nucleotide sequences of mcr-1.35 and mcr-1.36 presented 95.33 and 95.33% identities, respectively, to mcr-1.1. The phylogenetic analysis showed that mcr-1.35 and mcr-1.36 were derived from Moraxella spp. that belonged to subclades that were different from those of the mcr-1 variants (mcr-1.1 to mcr-1.34 except mcr-1.10) originating from Enterobacteriaceae. The deduced amino acid sequences of MCR-1.35 (MCR-1.36) showed 96.67% (96.49%), 82.59% (82.04%), 84.07% (83.52%), 55.52% (55.17%), 59.75% (59.57%), and 61.88% (61.69%) identity to MCR-1.10, MCR-2.2, MCR-6.1, MCR-LIN, MCR-OSL, and MCR-POR, respectively, that originated from Moraxella sp. Notably, protein structure alignment showed only a few changes in amino acid residues between MCR-1.1 and MCR-1.35, as well as between MCR-1.1 and MCR-1.36. In conclusion, this study identified Moraxella spp. carrying two novel mcr-1 variants, mcr-1.35 and mcr-1.36, conferring resistance to colistin, which were isolated from pig farms in China. In addition, mcr-like variants were observed to be located in the chromosomes of some species of Moraxella isolated from pig samples.

Colistin Resistance Genes in Broiler Chickens in Tunisia

Colistin is a polymyxin antibiotic that has been used in veterinary medicine for decades, as a treatment for enterobacterial digestive infections as well as a prophylactic treatment and growth promoter in livestock animals, leading to the emergence and spread of colistin-resistant Gram-negative bacteria and to a great public health concern, considering that colistin is one of the last-resort antibiotics against multidrug-resistant deadly infections in clinical practice. Previous studies performed on livestock animals in Tunisia using culture-dependent methods highlighted the presence of colistin-resistant Gram-negative bacteria. In the present survey, DNA extracted from cloacal swabs from 195 broiler chickens from six farms in Tunisia was tested via molecular methods for the ten mobilized colistin resistance (mcr) genes known so far. Of the 195 animals tested, 81 (41.5%) were mcr-1 positive. All the farms tested were positive, with a prevalence ranging from 13% to 93%. These results confirm the spread of colistin resistance in livestock animals in Tunisia and suggest that the investigation of antibiotic resistance genes by culture-independent methods could be a useful means of conducting epidemiological studies on the spread of antimicrobial resistance.

Farm to table: colistin resistance hitchhiking through food

Colistin is a high priority, last-resort antibiotic recklessly used in livestock and poultry farms. It is used as an antibiotic for treating multi-drug resistant Gram-negative bacterial infections as well as a growth promoter in poultry and animal farms. The sub-therapeutic doses of colistin exert a selection pressure on bacteria leading to the emergence of colistin resistance in the environment. Colistin resistance gene, mcr are mostly plasmid-mediated, amplifying the horizontal gene transfer. Food products such as chicken, meat, pork etc. disseminate colistin resistance to humans through zoonotic transfer. The antimicrobial residues used in livestock and poultry often leaches to soil and water through faeces. This review highlights the recent status of colistin use in food-producing animals, its association with colistin resistance adversely affecting public health. The underlying mechanism of colistin resistance has been explored. The prohibition of over-the-counter colistin sales and as growth promoters for animals and broilers has exhibited effective stewardship of colistin resistance in several countries.

Two-site study on performances of a commercially available MALDI-TOF MS-based assay for the detection of colistin resistance in Escherichia coli

Colistin is a last resort drug for the treatment of multiple drug-resistant (MDR) Gram-negative bacterial infections. Rapid methods to detect resistance are highly desirable. Here, we evaluated the performance of a commercially available MALDI-TOF MS-based assay for colistin resistance testing in Escherichia coli at two different sites. Ninety clinical E. coli isolates were provided by France and tested in Germany and UK using a MALDI-TOF MS-based colistin resistance assay. Lipid A molecules of the bacterial cell membrane were extracted using the MBT Lipid Xtract Kit™ (RUO; Bruker Daltonics, Germany). Spectra acquisition and evaluation were performed by the MBT HT LipidART Module of MBT Compass HT (RUO; Bruker Daltonics) on a MALDI Biotyper® sirius system (Bruker Daltonics) in negative ion mode. Phenotypic colistin resistance was determined by broth microdilution (MICRONAUT MIC-Strip Colistin, Bruker Daltonics) and used as a reference. Comparing the results of the MALDI-TOF MS-based colistin resistance assay with the data of the phenotypic reference method for the UK, sensitivity and specificity for the detection of colistin resistance were 97.1% (33/34) and 96.4% (53/55), respectively. Germany showed 97.1% (33/34) sensitivity and 100% (55/55) specificity for the detection of colistin resistance by MALDI-TOF MS. Applying the MBT Lipid Xtract™ Kit in combination with MALDI-TOF MS and dedicated software showed excellent performances for E. coli. Analytical and clinical validation studies must be performed to demonstrate the performance of the method as a diagnostic tool.

Gram-negative bacilli carrying mcr gene in Brazil: a pathogen on the rise

The incidence of infections caused by resistant Gram-negative pathogens has become a critical factor in public health due to the limitation of therapeutic options for the control of infections caused, especially, by Enterobacteriaceae (Escherichia coli and Klebsiella pneumoniae), Pseudomonas spp., and Acinetobacter spp. Thus, given the increase in resistant pathogens and the reduction of therapeutic options, polymyxins were reintroduced into the clinic. As the last treatment option, polymyxins were regarded as the therapeutic key, since they were one of the few classes of antimicrobials that had activity against multidrug-resistant Gram-negative bacilli. Nonetheless, over the years, the frequent use of this antimicrobial has led to reports of resistance cases. In 2015, mcr (mobile colistin resistance), a colistin resistance gene, was described in China. Due to its location on carrier plasmids, this gene is characterized by rapid spread through conjugation. It has thus been classified as a rising threat to public health worldwide. In conclusion, based on several reports that show the emergence of mcr in different regional and climatic contexts and species of isolates, this work aims to review the literature on the incidence of the mcr gene in Brazil in different regions, types of samples identified, species of isolates, and type of carrier plasmid.

Complete Genetic Analysis of Plasmids Carrying Multiple Resistance, Virulence, and Phage-Like Genes in Foodborne Escherichia coli Isolate

Bacterial antimicrobial resistance, especially phenotypic resistance to multiple drugs (MDR), has posed a serious threat to public health worldwide. To clarify the mechanism of transmission of multidrug resistance encoding plasmids in Enterobacterales, all seven plasmids of an Escherichia coli (E. coli) strain 1108 obtained from a chicken meat sample were extracted and sequenced by Illumina Nextseq 500 and MinION platforms. Plasmids in strain 1108 possessed 16 known antimicrobial resistance genes, with p1108-NDM (~97K) being the most variable plasmid. The multidrug resistance region of p1108-NDM was punctuated by eight IS26 insertion sequences; thus, four MDR regions were found in the backbone of this plasmid. The plasmid p1108-MCR (~65K) was found to lack the ISApl1 element and harbor the blaCTX-M-64-ISEcp1 transposition unit. Moreover, the ISEcp1-blaCMY-2 transposition unit was found in plasmid p1108-CMY2 (~98K), whereas plasmid p1108-emrB (~102K) was associated with resistance to erythromycin (emrB) and streptomycin (aadA22). p1108-IncY (96K) was a phage P1-like plasmid, while p1108-IncFIB (~194K) was found to harbor a virulence region similar to ColV plasmids, and they were found to encode a conserved conjugative transfer protein but harbor no resistance genes. Finally, no mobile element and resistant genes were found in p1108-ColV (~2K). Carriage of mcr-1-encoding elements in carbapenemase-producing Escherichia coli will potentially render all antimicrobial treatment regimens ineffective. Enhanced surveillance and effective intervention strategies are urgently needed to control the transmission of such multidrug resistance plasmids. IMPORTANCE Antimicrobial resistance (AMR) has been increasingly prevalent in agricultural and clinical fields. Understanding the genetic environment involved in AMR genes is important for preventing transmission and developing mitigation strategies. In this study, we investigated the genetic features of an E. coli strain (1108) isolated from food product and harboring 16 AMR genes, including blaNDM-1 and mcr-1 genes encoding resistance to last line antibiotics, meropenem, and colistin. Moreover, this strain also carried virulence genes such as iroBCDEN, iucABCD, and iutA. Our findings confirmed that multiple conjugative plasmids that were formed through active recombination and translocation events were associated with transmission of AMR determinants. Our data warrant the continuous monitoring of emergence and further transmission of these important MDR pathogens.

Plasmid-Mediated Colistin Resistance Genes mcr-1 and mcr-4 in Multidrug-Resistant Escherichia coli Strains Isolated from a Healthy Pig in Portugal

Antimicrobial resistance encoded by mobile colistin resistance (mcr) genes is a global and emergent threat. In this study, we report the occurrence of two different populations of colistin-resistant Escherichia coli harboring mcr-1 and mcr-4 variants in the intestinal microbiome of a healthy pig. Following antimicrobial susceptibility determination, the presence of mcr genes in two E. coli strains, isolated according to different selective microbiological procedures, was screened by PCR. Whole-genome sequencing confirmed that both strains were multidrug-resistant; INIAV_002EC was an AmpC producer carrying bla_CMY-2, bla_TEM-1B, qnrS1, mcr-1.1 genes, and INIAV_001EC carrying bla_TEM-1A, tetB, and mcr-4.1 genes, along with mutations in quinolone resistance-determining regions. In addition, both strains harbored sul3, dfrA, and aadA1 determinants. Further genome analysis revealed different plasmid replicons associated with the mcr genes, IncX4 associated with mcr-1.1, and ColE10 with mcr-4.1. In addition, other replicons, including IncFIA, IncI1-Iγ, IncX1, IncY, in INIAV_002EC, and IncX1, IncI1, and p0111, in INIAV_001EC, were identified. Furthermore, both strains belonged to ST215 serotype O68:H12 and ST156 serotype O25:H28, respectively. This finding highlights the pig gut flora as a potential reservoir of mobile colistin resistance genes and reports the presence of the mcr-4.1 gene found for the first time in Portugal.