scholarly journals Convergence of MCR-8.2 and chromosome-mediated resistance to colistin and tigecycline in an NDM-5-producing ST656 Klebsiella pneumoniae from a lung transplant patient

2021 ◽  
Author(s):  
Jiankang Zhao ◽  
Ziyao Li ◽  
Yulin Zhang ◽  
Xinmeng Liu ◽  
Zhujia Xiong ◽  
...  

For infection caused by NDM-5-producing Klebsiella pneumoniae, tigecycline and colistin are the last treatment options. In this study, we characterized the first NDM-5 and MCR-8.2 co-harboring K. pneumoniae clinical isolate, combining with chromosomal gene-mediated resistance to colistin and tigecycline. The K. pneumoniae KP32558 was isolated from the bronchoalveolar lavage fluid from a lung transplant male patient. Whole genome sequencing was carried out using Illumina HiSeq sequencing platform as well as nanopore sequencing method. The K. pneumoniae KP32558 was identified as a pan-drug resistant bacteria, belonged to ST656, and harbored plasmid-encoded blaNDM-5 and mcr-8.2 genes. The blaNDM-5 gene was located on an IncX3 type plasmid, which was successfully transferred to Escherichia coli strain J53 without visible fitness cost. The mcr-8.2 gene was located on a conjugative plasmid pKP32558-2-mcr8. It had two replicons, IncFII(K) and IncQ1, harbored previously by another two mcr-8.2-carrying plasmids pMCR8_020135 and pMCR8_095845. These three plasmids were clustered into the same clade and derived from K. pneumoniae isolates of the same clonal complex, indicating that pKP32558-2-mcr8 may come from pMCR8_020135 and pMCR8_095845 related ancestor. The MIC of KP32558 for colistin was 256 mg/L, the 6 amino acid substitutions in the two-component system may involve in the high-level colistin resistance. The truncation in acrR gene, related to tigecycline resistance, was also identified. K. pneumoniae has evolved a variety of complex resistance mechanisms to the last-resort antimicrobials, close surveillance is urgently needed to monitor the prevalence of this clone.

2021 ◽  
Vol 70 (4) ◽  
Author(s):  
Balaram Khamari ◽  
Prakash Kumar ◽  
Bulagonda Eswarappa Pradeep

Introduction. Nitrofurantoin is one of the preferred antibiotics in the treatment of uropathogenic multidrug-resistant (MDR) infections. However, resistance to nitrofurantoin in extensively drug-resistant (XDR) bacteria has severely limited the treatment options. Gap statement. Information related to co-resistance or collateral sensitivity (CS) with reference to nitrofurantoin resistant bacteria is limited. Aim. To study the potential of nitrofurantoin resistance as an indicator of the XDR phenotype in Enterobacteriaceae . Methods. One hundred (45 nitrofurantoin-resistant, 21 intermediately resistant and 34 nitrofurantoin-susceptible) Enterobacteriaceae were analysed in this study. Antibiotic susceptibility testing (AST) against nitrofurantoin and 17 other antimicrobial agents across eight different classes was performed by using the Vitek 2.0 system. The isolates were screened for the prevalence of acquired antimicrobial resistance (AMR) and efflux pump genes by PCR. Results. In total, 51 % of nitrofurantoin-resistant and 28 % of intermediately nitrofurantoin resistant isolates exhibited XDR characteristics, while only 3 % of nitrofurantoin-sensitive isolates were XDR (P=0.0001). Significant co-resistance was observed between nitrofurantoin and other tested antibiotics (β-lactam, cephalosporin, carbapenem, aminoglycoside and tetracycline). Further, the prevalence of AMR and efflux pump genes was higher in the nitrofurantoin-resistant strains compared to the susceptible isolates. A strong association was observed between nitrofurantoin resistance and the presence of bla PER-1, bla NDM-1, bla OXA-48, ant(2) and oqxA-oqxB genes. Tigecycline (84 %) and colistin (95 %) were the only antibiotics to which the majority of the isolates were susceptible. Conclusion. Nitrofurantoin resistance could be an indicator of the XDR phenotype among Enterobacteriaceae , harbouring multiple AMR and efflux pump genes. Tigecycline and colistin are the only antibiotics that could be used in the treatment of such XDR infections. A deeper understanding of the co-resistance mechanisms in XDR pathogens and prescription of AST-based appropriate combination therapy may help mitigate this problem.


2021 ◽  
Vol 12 ◽  
Author(s):  
Xueya Zhang ◽  
Qiaoling Li ◽  
Hailong Lin ◽  
Wangxiao Zhou ◽  
Changrui Qian ◽  
...  

Aminoglycosides are important options for treating life-threatening infections. However, high levels of aminoglycoside resistance (HLAR) among Klebsiella pneumoniae isolates have been observed to be increasing frequently. In this study, a total of 292 isolates of the K. pneumoniae complex from a teaching hospital in China were analyzed. Among these isolates, the percentage of HLAR strains was 13.7% (40/292), and 15 aminoglycoside resistance genes were identified among the HLAR strains, with rmtB being the most dominant resistance gene (70%, 28/40). We also described an armA-carrying Klebsiella variicola strain KP2757 that exhibited a high-level resistance to all aminoglycosides tested. Whole-genome sequencing of KP2757 demonstrated that the strain contained one chromosome and three plasmids, with all the aminoglycoside resistance genes (including two copies of armA and six AME genes) being located on a conjugative plasmid, p2757-346, belonging to type IncHI5. Comparative genomic analysis of eight IncHI5 plasmids showed that six of them carried two copies of the intact armA gene in the complete or truncated Tn1548 transposon. To the best of our knowledge, for the first time, we observed that two copies of armA together with six AME genes coexisted on the same plasmid in a strain of K. variicola with HLAR. Comparative genomic analysis of eight armA-carrying IncHI5 plasmids isolated from humans and sediment was performed, suggesting the potential for dissemination of these plasmids among bacteria from different sources. These results demonstrated the necessity of monitoring the prevalence of IncHI5 plasmids to restrict their worldwide dissemination.


2020 ◽  
Vol 8 (9) ◽  
pp. 1392 ◽  
Author(s):  
Maria J. Pons ◽  
Marta Marí-Almirall ◽  
Barbara Ymaña ◽  
Jeel Moya-Salazar ◽  
Laura Muñoz ◽  
...  

The aim of this study was to characterize carbapenem-resistant Klebsiella pneumoniae (CR-Kp) isolates recovered from adults and children with severe bacteremia in a Peruvian Hospital in June 2018. Antimicrobial susceptibility was determined by disc/gradient diffusion and broth microdilution when necessary. Antibiotic resistance mechanisms were evaluated by PCR and DNA sequencing. Clonal relatedness was assessed using pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Plasmid typing was performed with a PCR-based method. Thirty CR-Kp isolates were recovered in June 2018. All isolates were non-susceptible to all β-lactams, ciprofloxacin, gentamicin and trimethoprim-sulfamethoxazole, while mostly remaining susceptible to colistin, tigecycline, levofloxacin and amikacin. All isolates carried the blaNDM-1 gene and were extended spectrum β-lactamase (ESBL) producers. PFGE showed four different pulsotypes although all isolates but two belonged to the ST348 sequence type, previously reported in Portugal. blaNDM-1 was located in an IncFIB-M conjugative plasmid. To our knowledge, this is the first report of an New Delhi metallo-β-lactamase (NDM)-producing K. pneumoniae recovered from both children and adults in Lima, Peru, as well as the first time that the outbreak strain ST348 is reported in Peru and is associated with NDM. Studies providing epidemiological and molecular data on CR-Kp in Peru are essential to monitor their dissemination and prevent further spread.


mSphere ◽  
2020 ◽  
Vol 5 (2) ◽  
Author(s):  
Refath Farzana ◽  
Lim S. Jones ◽  
Andrew Barratt ◽  
Muhammad Anisur Rahman ◽  
Kirsty Sands ◽  
...  

ABSTRACT 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, blaTEM-1b and blaCTX-M-15, by IS903B. Coincidentally, all resistance determinants in the plasmid [mcr-8.1, ampC, sul2, 1d-APH(6), APH(3′′)-Ib, blaTEM-1b, blaCTX-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 blaCTX-M-15 and blaNDM 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.


Author(s):  
E.A. Kolesnikova ◽  
N.F. Brusnigina ◽  
G.I. Grigor’eva

Urogenital mycoplasmas (Mycoplasma genitalium, Mycoplasma hominis and Ureaplasma spp.) currently prevail in the etiology of infections of the urogenital tract and are characterized by a high level of genetic polymorphism responsible for the occurrence of their antibiotic resistance. The review presents the data of domestic and foreign researchers on the resistance mechanisms of mycoplasmas and ureaplasmas to antibiotics and considers the acquisition by mycoplasmas of antibiotic resistance determinants. New knowledge of resistance mechanisms is important theoretical basis for improving measures to limit and prevent the spread of antibiotic resistant bacteria.


Author(s):  
Mariana Castanheira ◽  
Timothy B Doyle ◽  
Timothy D Collingsworth ◽  
Helio S Sader ◽  
Rodrigo E Mendes

Abstract Objectives To investigate the increase in the rates of OXA-48-like-producing isolates during 3 years of global surveillance. Methods Among 55?>162 Enterobacterales isolates, 354 carbapenem-resistant isolates carried genes encoding OXA-48-like enzymes. Isolates were susceptibility tested for ceftazidime/avibactam and comparators by broth microdilution methods. Analysis of β-lactam resistance mechanisms and MLST was performed in silico using WGS data. Results OXA-48-like-producing isolates increased from 0.5% (94/18 656) in 2016 to 0.9% (169/18?>808) in 2018. OXA-48 was the most common variant; isolates primarily were Klebsiella pneumoniae (318/354 isolates) from Europe and adjacent countries. MLST analysis revealed a diversity of STs, but K. pneumoniae belonging to ST395, ST23 and ST11 were observed most frequently. Thirty-nine isolates harboured MBLs and were resistant to most agents tested. The presence of blaCTX-M-15 (258 isolates), OmpK35 nonsense mutations (232) and OmpK36 alterations (316) was common among OXA-48 producers. Ceftazidime, cefepime and aztreonam susceptibility rates, when applying CLSI breakpoints, were 12%–15% lower for isolates carrying ESBLs alone and with either or both OmpK35 stop codons and OmpK36 alterations. Meropenem and, remarkably, meropenem/vaborbactam were affected by specific OmpK36 alterations when a deleterious mutation also was observed in OmpK35. These mechanisms caused a decrease of 12%–42% in the susceptibility rates for meropenem and meropenem/vaborbactam. Ceftazidime/avibactam susceptibility rates were >98.9%, regardless of the presence of additional β-lactam resistance mechanisms. Conclusions Guidelines for the treatment of infections caused by OXA-48-producing isolates are scarce and, as the dissemination of these isolates continues, studies are needed to help physicians understand treatment options for these infections.


2017 ◽  
Author(s):  
Andre Mu ◽  
Jason C. Kwong ◽  
Nicole S. Isles ◽  
Anders Gonçalves da Silva ◽  
Mark B. Schultz ◽  
...  

AbstractWhole-genome sequencing of microbial pathogens is revolutionising modern approaches to outbreaks of infectious diseases and is reliant upon organism culture. Culture-independent methods have shown promise in identifying pathogens, but high level reconstruction of microbial genomes from microbiologically complex samples for more in-depth analyses remains a challenge. Here, using metagenomic sequencing of a human faecal sample and analysis by tetranucleotide frequency profiling projected onto emergent self-organising maps, we were able to reconstruct the underlying populations of two extensively-drug resistant pathogens, Klebsiella pneumoniae carbapenemase (KPC)-producing Klebsiella pneumoniae and vancomycin-resistant Enterococcus faecium. From these genomes, we were able to ascertain molecular typing results, such as MLST, and identify highly discriminatory mutations in the metagenome to distinguish closely related strains. These proof-of-principle results demonstrate the utility of clinical sample metagenomics to recover sequences of important drug-resistant bacteria and application of the approach in outbreak investigations, independent of the need to culture the organisms.


Microbiome ◽  
2020 ◽  
Vol 8 (1) ◽  
Author(s):  
Maria-Elisabeth Böhm ◽  
Mohammad Razavi ◽  
Nachiket P. Marathe ◽  
Carl-Fredrik Flach ◽  
D. G. Joakim Larsson

Abstract Background New antibiotic resistance determinants are generally discovered too late, long after they have irreversibly emerged in pathogens and spread widely. Early discovery of resistance genes, before or soon after their transfer to pathogens could allow more effective measures to monitor and reduce spread, and facilitate genetics-based diagnostics. Results We modified a functional metagenomics approach followed by in silico filtering of known resistance genes to discover novel, mobilised resistance genes in class 1 integrons in wastewater-impacted environments. We identified an integron-borne gene cassette encoding a protein that conveys high-level resistance against aminoglycosides with a garosamine moiety when expressed in E. coli. The gene is named gar (garosamine-specific aminoglycoside resistance) after its specificity. It contains none of the functional domains of known aminoglycoside modifying enzymes, but bears characteristics of a kinase. By searching public databases, we found that the gene occurs in three sequenced, multi-resistant clinical isolates (two Pseudomonas aeruginosa and one Luteimonas sp.) from Italy and China, respectively, as well as in two food-borne Salmonella enterica isolates from the USA. In all cases, gar has escaped discovery until now. Conclusion To the best of our knowledge, this is the first time a novel resistance gene, present in clinical isolates, has been discovered by exploring the environmental microbiome. The gar gene has spread horizontally to different species on at least three continents, further limiting treatment options for bacterial infections. Its specificity to garosamine-containing aminoglycosides may reduce the usefulness of the newest semisynthetic aminoglycoside plazomicin, which is designed to avoid common aminoglycoside resistance mechanisms. Since the gene appears to be not yet common in the clinics, the data presented here enables early surveillance and maybe even mitigation of its spread.


2019 ◽  
Vol 74 (8) ◽  
pp. 2225-2229 ◽  
Author(s):  
Li-Hua Li ◽  
Man-San Zhang ◽  
Chao-Jung Wu ◽  
Yi-Tsung Lin ◽  
Tsuey-Ching Yang

Abstract Background Stenotrophomonas maltophilia displays high-level resistance to various antibiotics. Fluoroquinolone is among the few treatment options for S. maltophilia infection. Overexpression of SmeDEF, SmeVWX and SmQnr are the main mechanisms responsible for fluoroquinolone resistance in S. maltophilia. Objectives To reveal the unidentified fluoroquinolone resistance mechanisms in S. maltophilia. Methods Fluoroquinolone-resistant spontaneous mutants were selected by spreading KJΔDEFΔ5, a SmeDEF- and SmeVWX-null double mutant, on ciprofloxacin- or levofloxacin-containing medium. Antibiotic susceptibility was assessed by the agar dilution method. Outer membrane protein profiles of fluoroquinolone-resistant mutants were assayed by SDS-PAGE and significant protein was characterized by LC-MS/MS. The expression of tolCsm, smeH, smeK, smeN, smeP, smeZ and smQnr was investigated by real-time quantitative PCR. The contribution of SmeGH overexpression to antibiotic resistance was verified by ΔsmeH mutant construction and smeGH complementation assay. Results Most fluoroquinolone-resistant mutants displayed MDR. The TolCsm protein and smeH transcript were concomitantly overexpressed in some MDR mutants. smeH deletion increased the susceptibility of the MDR mutants to fluoroquinolone, macrolide, chloramphenicol and tetracycline, and the resistance compromise was partially reversed by complementation with a plasmid containing smeGH. SmeGH overexpression was found in some fluoroquinolone-resistant clinical S. maltophilia isolates whose SmeDEF, SmeVWX and SmQnr proteins were not or were lowly expressed. Conclusions Overexpression of SmeGH contributes to the acquired resistance of S. maltophilia to fluoroquinolone, macrolide, chloramphenicol and tetracycline.


2021 ◽  
Author(s):  
Shewli Mukerji ◽  
Shafi Sahibzada ◽  
Rebecca Abraham ◽  
Marc Stegger ◽  
David Jordan ◽  
...  

AbstractHuman population and activities play an important role in dissemination of antimicrobial resistant bacteria. This study investigated the relationship between carriage rates of critically important antimicrobial-resistant (CIA-R) Escherichia coli and Klebsiella pneumoniae by Silver Gulls and their proximity to human populations. Faecal swabs (n=229) were collected from Silver Gulls across 10 southern coastline locations in Western Australia (WA). The sampling locations included main town centres and remote areas. Fluoroquinolone and extended-spectrum cephalosporin-resistant E. coli and K. pneumoniae were isolated and tested for antimicrobial sensitivity. Genome sequencing was performed to validate phenotypic resistance profiles and determine the molecular characteristics of strains. CIA-R E. coli and K. pneumoniae were detected in 69 (30.1%) and 20 (8.73%) of the faecal swabs respectively. Two large urban locations tested positive for CIA-R E. coli (frequency ranging from 34.3%-84.3%), and/or for CIA-R K. pneumoniae (frequency ranging from 12.5%-50.0%). A small number of CIA-R E. coli (3/31, 9.7%) were identified at a small tourist town, but no CIA-R bacteria were recovered from gulls at remote sites. Commonly detected E. coli sequence types (STs) included ST131 (12.5%) and ST1193 (10.0%), and five K. pneumoniae STs were found. Resistance genes including blaCTX-M-3, blaCTX-M-15 and blaCTX-M-27 were identified in both bacterial species. High-level colonisation of CIA-R E. coli and K. pneumoniae in Silver Gulls in and around urban areas compared to remote locations substantiates that anthropogenic activities are strongly associated with acquisition of resistant bacteria by gulls.ImportanceHumans play an important role in dissemination of antimicrobial resistant bacteria. This study investigated the relationship between carriage rates of resistant bacterial pathogens (Escherichia coli and Klebsiella pneumoniae) among Silver Gulls and their proximity to human populations. The frequency of resistant E. coli carriage was high (ranging from 34.3 – 84.3%) in the samples collected from areas with high human population density while resistant K. pneumoniae frequencies at these sites varied from 0 to 50%. However, resistant E. coli and K. pneumoniae were not recovered from any of the remote sites that did not have a permanent human population. This study, conducted across a large stretch of the southwestern Australian coastline, indicated that seagulls act as vectors in carrying and disseminating antimicrobial resistant bacteria, including clinically significant strains. High-level colonisation of resistant E. coli and K. pneumoniae in Silver Gulls in and around urban areas compared to remote locations substantiates that human activities are strongly associated with acquisition of resistant bacteria by Silver gulls.


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