Abiola Olumuyiwa Olaitan

Mechanisms of polymyxin resistance: acquired and intrinsic resistance in bacteria

Polymyxins are polycationic antimicrobial peptides that are currently the last-resort antibiotics for the treatment of multidrug-resistant, Gram-negative bacterial infections. The reintroduction of polymyxins for antimicrobial therapy has been followed by an increase in reports of resistance among Gram-negative bacteria. Some bacteria, such as Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii, develop resistance to polymyxins in a process referred to as acquired resistance, whereas other bacteria, such as Proteus spp., Serratia spp., and Burkholderia spp., are naturally resistant to these drugs. Reports of polymyxin resistance in clinical isolates have recently increased, including acquired and intrinsically resistant pathogens. This increase is considered a serious issue, prompting concern due to the low number of currently available effective antibiotics. This review summarizes current knowledge concerning the different strategies bacteria employ to resist the activities of polymyxins. Gram-negative bacteria employ several strategies to protect themselves from polymyxin antibiotics (polymyxin B and colistin), including a variety of lipopolysaccharide (LPS) modifications, such as modifications of lipid A with phosphoethanolamine and 4-amino-4-deoxy-L-arabinose, in addition to the use of efflux pumps, the formation of capsules and overexpression of the outer membrane protein OprH, which are all effectively regulated at the molecular level. The increased understanding of these mechanisms is extremely vital and timely to facilitate studies of antimicrobial peptides and find new potential drugs targeting clinically relevant Gram-negative bacteria.

Dissemination of the mcr-1 colistin resistance gene

www.thelancet.com/infection Vol 16 March 2016 289 1 Liu Y-Y, Wang Y, Walsh TR, et al. Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study. Lancet Infect Dis 2016; 16: 161–68. 2 Paterson DL, Harris PN. Colistin resistance: a major breach in our last line of defence. Lancet Infect Dis 2016; 16: 132–33. 3 Li J, Nation RL, Turnidge JD, et al. Colistin: the re-emerging antibiotic for multidrug-resistant Gram-negative bacterial infections. Lancet Infect Dis 2006; 6: 589–601. 4 Wang X, Li H, Zhao C, et al. Novel NDM-9 metallo-β-lactamase identifi ed from a ST107 Klebsiella pneumoniae strain isolated in China. Int J Antimicrob Agents 2014; 44: 90–91. 5 Yang X, Liu W, Liu Y, et al. F33: A-: B-, IncHI2/ST3, and IncI1/ST71 plasmids drive the dissemination of fosA3 and blaCTX-M-55/-14/-65 in Escherichia coli from chickens in China. Front Microbiol 2014; 5: 688. 6 He L, Partridge SR, Yang X, et al. Complete nucleotide sequence of pHN7A8, an F33:A-:Btype epidemic plasmid carrying blaCTX-M-65, fosA3 and rmtB from China. J Antimicrob Chemother 2013; 68: 46–50. plasmids to other Gram-negative pathogens, which might result in untreatable infections. Thus, the spread of mcr-1, especially into strains that are already resistant to carbapenems, must be stopped.Plasmid-mediated transferable colistin resistance encoded by the mcr-1 gene was described in Escherichia coli and Klebsiella pneumoniae isolates from pigs and chicken at a prevalence of around 20%, and in clinical isolates from human beings at a prevalence of around 1% in China. The prevalence of the mcr-1 gene in Enterobacteriaceae in other countries and in the community is unknown. We did a prospective study of acquisition of fecal colonisation and carriage with extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae in 2001 Dutch travellers (the COMBAT study), from November, 2012, to November, 2013. Acquisition was defi ned as the absence of ESBLproducing Enterobacteriaceae in a fecal swab sample taken immediately before travel and detection of ESBL-producing Enterobacteriaceae in a sample taken within 1–2 weeks after return to the Netherlands. Of 1847 travellers at risk, 633 (34%) acquired ESBL-producing Enterobacteriaceae. Nine of these 633 travellers acquired ESBL-producing Escherichia coli with a colistin minimum inhibitory concentration of 4–8 mg/L (EUCAST clinical breakpoint for resistance >2 mg/L) as detected using Vitek-2 and confi rmed by E-test. After publication of the report by Yi-Yun Liu and colleagues, these nine isolates were tested by PCR for the presence of the mcr-1 gene. The gene was detected in six of nine isolates and sequencing of the amplicons showed a 100% homology over the length of the fragments with the published sequence. Three ESBL-producing E coli were mcr-1 PCR negative, suggesting colistin resistance due to other mechanisms. Analysis of ESBL genes by microarray, PCR, and sequencing showed that the mcr-1 positive ESBLproducing E coli carried ESBL genes belonging to multiple groups (table). Of the six travellers who acquired ESBL-producing E coli carrying the mcr-1 gene, two unrelated travellers visited Peru and Bolivia, two unrelated travellers visited China, one visited Tunisia, and one visited multiple countries in southeast Asia (Thailand, Vietnam, Laos, and Cambodia). The duration of travel ranged between 8 and 40 days (mean 21·3 days). None of the travellers had accessed medical care and none had used antimicrobial drugs during travel, while five had experienced traveller’s diarrhoea. Analysis of subsequent fecal samples collected at 1, 3, 6, and 12 months after return to the Netherlands did not show ESBLproducing E coli, suggesting shortterm colonisation with colistin resistant ESBL-producing E coli or loss of plasmids carrying ESBL and potentially mcr-1 genes. Lancet Infect Dis 2015

Worldwide emergence of colistin resistance in Klebsiella pneumoniae from healthy humans and patients in Lao PDR, Thailand, Israel, Nigeria and France owing to inactivation of the PhoP/PhoQ regulator mgrB: an epidemiological and molecular study

The emergence of colistin-resistant Klebsiella pneumoniae (CRKP) is a major public health concern worldwide. In this study, the prevalence and molecular basis of colistin resistance in CRKP isolated from healthy individuals and patients in Lao PDR, Thailand, Nigeria and France were investigated. Stool samples were screened by culture for the presence of colistin-resistant Klebsiella spp. Whole-genome sequence analysis was used to decipher the molecular mechanism of colistin resistance in a blaNDM-1-positive in vitro-selected CRKP mutant. PCR amplification and sequencing of the mgrB genetic environment was performed for all CRKP isolates as well as control colistin-susceptible K. pneumoniae (CSKP) isolates recovered from the same stools. A total of 869 stool samples were screened for colistin-resistant Klebsiella spp., yielding 32 CRKP and 2 colistin-resistant Klebsiella oxytoca. Comparative whole-genome sequence analysis revealed that an in vitro-selected CRKP mutant had an insertion sequence in its mgrB gene, as well as missense mutations in other selected clones. Of the 34 colistin-resistant Klebsiella spp. isolates, 14 (41.2%; 13 CRKP and 1 K. oxytoca) from the four countries also had various defects in their mgrB genes, but no such defects were found in the CSKP controls (P<10(-4)). Few mutations were observed in pmrAB compared with mgrB among the CRKP isolates. The worldwide emergence of CRKP is a major public health concern. Detection and surveillance of such strains are warranted to prevent an uncontrollable pandemic. Inactivation of the PhoP/PhoQ regulator gene mgrB is associated with ≥40% of colistin resistance among the CRKP isolates observed in this study.

Molecular mechanisms of polymyxin resistance: knowns and unknowns

Colistin, also referred to as polymyxin E, is an effective antibiotic against most multidrug-resistant Gram-negative bacteria and is currently used as a last-line drug for treating severe bacterial infections. Colistin resistance has increased gradually for the last few years, and knowledge of its multifaceted mechanisms is expanding. This includes the newly discovered plasmid-mediated colistin resistance gene mcr-1, which has been detected in over 20 countries within 3 months of its first report. We previously reported all of the known mechanisms of polymyxin resistance in our first review in 2014, but an update seems necessary in 2016, considering the significant recent discoveries that have been made in this domain. This review provides an update about what is already known, what is new, and some unresolved questions with respect to colistin resistance.

Acquisition of extended-spectrum cephalosporin- and colistin-resistant Salmonella enterica subsp. enterica serotype Newport by pilgrims during Hajj

Gatherings like the Hajj involving many people who travel from different parts of the world represent a risk for the acquisition and dissemination of infectious diseases. In this study, acquisition of multidrug-resistant (MDR) Salmonella spp. in 2013 Hajj pilgrims from Marseille, France, was investigated. In total, 267 rectal swabs were collected from 129 participants before their departure and after their return from the pilgrimage as well as during the pilgrimage from patients with diarrhoea. Samples were screened for the presence of Salmonella using quantitative real-time PCR and culture. Whole-genome sequencing was performed to characterise one of the isolates, and the mechanism leading to colistin resistance was investigated. Six post-Hajj samples and one sample collected during a diarrhoea episode in Hajj were positive for Salmonella by real-time PCR, with five Salmonella enterica belonging to several serotypes recovered by culture, whereas no pre-Hajj sample was positive. Two of the isolates belonged to the epidemic Newport serotype, were resistant to cephalosporins, gentamicin and colistin, and harboured the bla(CTX-M-2) gene and a 12-nucleotide deletion in the pmrB gene leading to colistin resistance. This study shows that pilgrims acquired Salmonella bacteria, including a novel MDR clone, during the Hajj pilgrimage. This calls for more improved public health surveillance during Hajj because Salmonella is one of the most common diarrhoea-causing bacteria worldwide. Therefore, returning pilgrims could disseminate MDR bacteria worldwide upon returning to their home countries.

Clonal transmission of a colistin-resistant #Escherichia coli# from a domesticated pig to a human in Laos

Sir,Colistin, recently reintroduced in human medicine, is one ofthe most important antibiotics currently used to treat severeGram-negative bacterial infections in humans. Unfortunately, it isalso extensively used in animal production, including in swineandpoultryfarmingagainstGram-negativebacterialpathogens.

Emergence of multidrug-resistant Acinetobacter baumannii producing OXA-23 carbapenemase, Nigeria

The objective of our study was to describe the molecular support of carbapenem resistance from randomly selected clinical isolates of multidrug-resistant (MDR) Acinetobacter baumannii as a pilot study from the Hamad Medical Corporation (HMC), Qatar. Results of our report will be used to study carbapenemases using molecular techniques in all isolated MDR A. baumannii. Forty-eight MDR A. baumannii were randomly selected from isolates preserved at HMC. Identification of all isolates was confirmed by matrix-assisted laser desorption/ ionization time-of-flight mass spectrometry. Antibiotic resistance was tested phenotypically by Phoenix and confirmed by Etest. The molecular support of carbapenemases (blaOXA-23, blaOXA-24, blaOXA-58, blaNDM) was investigated by real-time PCR. The epidemiologic relatedness of the isolates was verified by phylogenetic analysis based on partial sequences of CsuE and blaOXA-51 genes. All 48 isolates were identified as A. baumannii and were confirmed to be resistant to most antibiotics, especially meropenem, imipenems, ciprofloxacin, levofloxacin, amikacin, gentamicin and most of the β-lactams; they were sensitive to colistin. All the isolates were positive for blaOXA-23 and negative for the other tested carbapenemase genes. Clonality analysis demonstrated that different lineages were actually circulating in Qatar; and we suggest that an outbreak occurred in the medical intensive care unit of HMC between 2011 and 2012. Here we report the emergence of MDR A. baumannii producing the carbapenemase OXA-23 in Qatar. New Microbes and New Infections

Plasmid-Mediated mcr-1 Gene in Colistin-Resistant Clinical Isolates of Klebsiella pneumoniae in France and Laos

Recently, Yi-Yun Liu et al. reported the emergence of plasmid-mediated colistin resistance involving the mcr-1 gene from Escherichia coli and Klebsiella pneumoniae isolates from animals, food, and humans in China ([1][1]). Because of the plasmidic location of this new gene, which encodes a

Acquisition of Extended-Spectrum β-Lactamases by Escherichia coli and Klebsiella pneumoniae in Gut Microbiota of Pilgrims during the Hajj Pilgrimage of 2013

ABSTRACT We reported the acquisition of extended-spectrum-β-lactamase (ESBL)-producing bacteria in rectal samples of 129 pilgrims during the 2013 Hajj (pilgrimage to Makkah). When returning from the Hajj, there was a significant increase in the number of pilgrims carrying E. coli resistant to ceftriaxone (P = 0.008). The CTX-M gene was detected in rectal samples, with the detection rate increasing from 10.08% to 32.56% of samples after the Hajj (P < 0.001).

Whole genome sequence to decipher the resistome of Shewanella algae, a multidrug-resistant bacterium responsible for pneumonia, Marseille, France

We characterize and decipher the resistome and the virulence factors of Shewanella algae MARS 14, a multidrug-resistant clinical strain using the whole genome sequencing (WGS) strategy. The bacteria were isolated from the bronchoalveolar lavage of a hospitalized patient in the Timone Hospital in Marseille, France who developed pneumonia after plunging into the Mediterranean Sea. Results: The genome size of S. algae MARS 14 was 5,005,710 bp with 52.8% guanine cytosine content. The resistome includes members of class C and D beta-lactamases and numerous multidrug-efflux pumps. We also found the presence of several hemolysins genes, a complete flagellum system gene cluster and genes responsible for biofilm formation. Moreover, we reported for the first time in a clinical strain of Shewanella spp. the presence of a bacteriocin (marinocin). Conclusion: The WGS analysis of this pathogen provides insight into its virulence factors and resistance to antibiotics.