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genetics of antimicrobial resistance

Monica M Lahra, Irene Martin, Walter Demczuk, Amy V Jennison, Ken-Ichi Lee, Shu-Ichi Nakayama, Brigitte Lefebvre, Jean Longtin, Alison Ward, Michael R Mulvey, Teodora Wi, Makoto Ohnishi, David Whiley
Ceftriaxone remains a first-line treatment for patients infected by Neisseria gonorrhoeae in most settings. We investigated the possible spread of a ceftriaxone-resistant FC428 N. gonorrhoeae clone in Japan after recent isolation of similar strains in Denmark (GK124) and Canada (47707). We report 2 instances of the FC428 clone in Australia in heterosexual men traveling from Asia. Our bioinformatic analyses included core single-nucleotide variation phylogeny and in silico molecular typing; phylogenetic analysis showed close genetic relatedness among all 5 isolates...
April 2018: Emerging Infectious Diseases
David Williams, Joanne L Fothergill, Benjamin Evans, Jessica Caples, Sam Haldenby, Martin J Walshaw, Michael A Brockhurst, Craig Winstanley, Steve Paterson
Pseudomonas aeruginosa chronic infections of cystic fibrosis (CF) airways are a paradigm for within-host evolution with abundant evidence for rapid evolutionary adaptation and diversification. Recently emerged transmissible strains have spread globally, with the Liverpool Epidemic Strain (LES) the most common strain infecting the UK CF population. Previously we have shown that highly divergent lineages of LES can be found within a single infection, consistent with super-infection among a cross-sectional cohort of patients...
March 16, 2018: Microbial Genomics
Jane Hawkey, David B Ascher, Louise M Judd, Ryan R Wick, Xenia Kostoulias, Heather Cleland, Denis W Spelman, Alex Padiglione, Anton Y Peleg, Kathryn E Holt
Acinetobacter baumannii is a common causative agent of hospital-acquired infections and a leading cause of infection in burns patients. Carbapenem-resistant A. baumannii is considered a major public-health threat and has been identified by the World Health Organization as the top priority organism requiring new antimicrobials. The most common mechanism for carbapenem resistance in A. baumannii is via horizontal acquisition of carbapenemase genes. In this study, we sampled 20 A. baumannii isolates from a patient with extensive burns, and characterized the evolution of carbapenem resistance over a 45 day period via Illumina and Oxford Nanopore sequencing...
March 16, 2018: Microbial Genomics
Pragathi B Shridhar, Isha R Patel, Jayanthi Gangiredla, Lance W Noll, Xiaorong Shi, Jianfa Bai, Christopher A Elkins, Nancy A Strockbine, T G Nagaraja
Escherichia coli O104:H4, a Shiga toxin-producing hybrid pathotype that was implicated in a major foodborne outbreak in Germany in 2011, has not been detected in cattle. However, serotypes of O104, other than O104:H4, have been isolated from cattle feces, with O104:H7 being the most predominant. In this study, we investigated, based on whole genome sequence analyses, the virulence potential of E. coli O104 strains isolated from cattle feces, since cattle are asymptomatic carriers of E. coli O104. The genomes of ten bovine E...
2018: Frontiers in Microbiology
Jin Yang Baek, Cheol-In Kang, So Hyun Kim, Kwan Soo Ko, Doo Ryeon Chung, Kyong Ran Peck, Nam Yong Lee, Jae-Hoon Song
The use of fluoroquinolones to treat respiratory tract infections and pneumonia due to Streptococcus pneumoniae has affected the emergence of resistance to this class of drugs. Increasing pneumococcal resistance to levofloxacin has become a major public health concern. We investigated the prevalence and genetic characteristics of levofloxacin-nonsusceptible S. pneumoniae (LNSP) clinical isolates in Korea. A total of 43 LNSP isolates collected from a national surveillance study at 13 tertiary hospitals between 2008 and 2014 were analyzed for serotype and antimicrobial susceptibilities to 19 antimicrobial agents as well as the quinolone resistance-determining region mutation...
February 16, 2018: Diagnostic Microbiology and Infectious Disease
Andrew J Page, Alexander Wailan, Yan Shao, Kim Judge, Gordon Dougan, Elizabeth J Klemm, Nicholas R Thomson, Jacqueline A Keane
Increasingly rich metadata are now being linked to samples that have been whole-genome sequenced. However, much of this information is ignored. This is because linking this metadata to genes, or regions of the genome, usually relies on knowing the gene sequence(s) responsible for the particular trait being measured and looking for its presence or absence in that genome. Examples of this would be the spread of antimicrobial resistance genes carried on mobile genetic elements (MGEs). However, although it is possible to routinely identify the resistance gene, identifying the unknown MGE upon which it is carried can be much more difficult if the starting point is short-read whole-genome sequence data...
March 12, 2018: Microbial Genomics
Alasdair T M Hubbard, Sian Davies, Laura Baxter, Sarah Thompson, Mark Collery, Daniel Hand, Daniel John Thomas, Colin Fink
Comparison of the genome of the Gram negative human pathogen Haemophilus quentini MP1 with other Haemophilus species revealed that, although it is more closely related to Haemophilus haemolyticus than Haemophilus influenzae, the pathogen is in fact genetically distinct, a finding confirmed by phylogenetic analysis using the H. influenzae multilocus sequence typing genes. Further comparison with two other H. quentini strains recently identified in Canada revealed that these three genomes are more closely related than any other Haemophilus species, however there is still some sequence variation...
March 13, 2018: Genome Génome / Conseil National de Recherches Canada
Bernard Louizette Christophe, Mariana Mott, Gabriela da Cunha, Juliana Caierão, Pedro D Azevedo, Cícero Dias
PURPOSE: Invasive pneumococcal disease (IPD) in the elderly is an important public health issue due to the increased proportion of this population in many countries including Brazil. We aimed to characterise pneumococci isolates in adults >50 years with IPD, following the introduction of the 10-valent pneumococcal conjugate vaccine (PCV10) as part of the National Childhood Immunisation Program for children ≤2 years in March 2010. METHODOLOGY: Between 2013 and 2015, pneumococcal isolates were collected and serotypes were determined using multiplex PCR and/or Quellung reaction...
March 13, 2018: Journal of Medical Microbiology
Susanne Sütterlin, Carlos J Téllez-Castillo, Leticia Anselem, Hong Yin, James E Bray, Martin C J Maiden
Antimicrobial resistance is a major health care problem, with the intensive use of heavy metals and biocides recently being identified as potential contributing factors to the aggravation of this situation. This study investigated heavy metal susceptibility and genetic resistance determinants in Escherichia coli isolated from clinical urine samples from Sweden, Germany and Spain. A total of 186 isolates were tested for minimal inhibition concentration to sodium arsenite, silver nitrate and copper (II) sulphate...
March 12, 2018: Antimicrobial Agents and Chemotherapy
William Gustavo Lima, Mara Cristina Alves, Waleska Stephanie Cruz, Magna Cristina Paiva
Acinetobacter baumannii is an opportunistic pathogen associated with nosocomial and community infections of great clinical relevance. Its ability to rapidly develop resistance to antimicrobials, especially carbapenems, has re-boosted the prescription and use of polymyxins. However, the emergence of strains resistant to these antimicrobials is becoming a critical issue in several regions of the world because very few of currently available antibiotics are effective in these cases. This review summarizes the most up-to-date knowledge about chromosomally encoded and plasmid-mediated polymyxins resistance in A...
March 9, 2018: European Journal of Clinical Microbiology & Infectious Diseases
Debi Prasad Mohapatra, Santosh Kumar Singh, Minu Sahoo, Shashank Patole, Mitali Mishra, Nagen Kumar Debata, Harapriya Mohapatra
PURPOSE: Antibiotic resistance patterns often exhibit geographical variations. Periodic analyses of resistance spectra and phylogenetic trends are important guides for facilitating judicious use of therapeutic interventions. The present study retrospectively analysed the infection trends, resistance patterns, and clonal relationships between isolates of Klebsiella spp. from a tertiary care hospital. METHODOLOGY: Bacterial isolates were collected from January 2013 to June 2014 and their resistance profiles were identified using an automated bacterial identification system...
March 9, 2018: Journal of Medical Microbiology
Qifa Song, Zhaojun Xu, Hong Gao, Danyang Zhang
Purpose: Several factors contribute to the complexity of quinolone resistance in Salmonella , including >2000 different Salmonella serotypes, a variety of hosts for Salmonella , and wide use of quinolones in human beings and animals. We thus aimed to obtain an overview of the development of quinolone resistance and relevant molecular mechanisms of such a resistance in Salmonella species. Materials and methods: A total of 1,776 Salmonella isolates were collected in Ningbo, China, between 2005 and 2016...
2018: Infection and Drug Resistance
Giulia Niero, Valeria Bortolaia, Michele Vanni, Luigi Intorre, Luca Guardabassi, Alessandra Piccirillo
The aim was to investigate occurrence and diversity of plasmid-mediated resistance to third-generation cephalosporins (3GC) and quinolones in clinical Escherichia coli from 200 industrial poultry farms across Italy. E. coli was isolated from colibacillosis lesions in turkeys (n = 109), broilers (n = 98) and layers (n = 22) between 2008 and 2012. 3GC-resistant isolates were screened for extended-spectrum and AmpC β-lactamase (ESBL/AmpC), while all isolates were tested for plasmid-mediated quinolone resistance (PMQR) genes...
March 2018: Veterinary Microbiology
Yoshihiko Maeyama, Yui Taniguchi, Wataru Hayashi, Yusuke Ohsaki, Shunsuke Osaka, Shota Koide, Kiyoko Tamai, Yukiko Nagano, Yoshichika Arakawa, Noriyuki Nagano
In recent years, besides the widespread occurrence of extended-spectrum β-lactamase (ESBL)- and/or plasmid-mediated AmpC (pAmpC)-producing Enterobacteriaceae in both healthcare and community settings of humans, the third-generation cephalosporin (3GC)-resistant microbes have also been reported from companion animals worldwide. Here, we characterized ESBL- and/or pAmpC-producing Enterobacteriaceae clinical isolates from companion animals. Among the 487 clinical isolates mainly from urine of dogs and cats between May and September 2016, 104 non-repetitive isolates were resistant to the 3GC, and they consisted of 81 of 381 (21...
March 2018: Veterinary Microbiology
Roya Ghanavati, Mohammad Emaneini, Davood Kalantar-Neyestanaki, Azin Sattari Maraji, Mosayyeb Dalvand, Reza Beigverdi, Fereshteh Jabalameli
INTRODUCTION: Here, we determined the genes encoding antibiotic resistance enzymes and virulence factors and evaluated the genetic relationship between Enterobacter spp. isolated from different clinical samples. METHODS: A total of 57 clinical isolates of Enterobacter spp. were tested for the production of extended-spectrum β-lactamases (ESBLs), carbapenemase, and AmpC using phenotypic and genotypic methods. RESULTS: The most common ESBLs and AmpC β-lactamases were bla TEM (63...
January 2018: Revista da Sociedade Brasileira de Medicina Tropical
Andrew Cameron, Cassidy L Klima, Reuben Ha, Robert J Gruninger, Rahat Zaheer, Tim A McAllister
A novel variant of the AAD(3″) class of aminoglycoside-modifying enzymes was discovered in fatal bovine respiratory disease-associated pathogens Pasteurella multocida and Histophilus somni . The aadA31 gene encodes a spectinomycin/streptomycin adenylyltransferase and was located in a variant of the integrative and conjugative element ICE Mh1 , a mobile genetic element transmissible among members of the family Pasteurellaceae . The gene was also detected in Mannheimia haemolytica from a case of porcine pneumonia and in Moraxella bovoculi from a case of keratoconjunctivitis...
January 2018: MSphere
Kara A Moser, Lixin Zhang, Ian Spicknall, Nikolay P Braykov, Karen Levy, Carl F Marrs, Betsy Foxman, Gabriel Trueba, William Cevallos, Jason Goldstick, James Trostle, Joseph N S Eisenberg
Small-scale production poultry operations are increasingly common worldwide. To investigate how these operations influence antimicrobial resistance and mobile genetic elements (MGEs), Escherichia coli isolates were sampled from small-scale production birds (raised in confined spaces with antibiotics in feed), household birds (no movement constraints; fed on scraps), and humans associated with these birds in rural Ecuador (2010-2012). Isolates were screened for genes associated with MGEs as well as phenotypic resistance to 12 antibiotics...
March 1, 2018: American Journal of Epidemiology
Diego B Nobrega, Sohail Naushad, S Ali Naqvi, Larissa A Z Condas, Vineet Saini, John P Kastelic, Christopher Luby, Jeroen De Buck, Herman W Barkema
Emergence and spread of antimicrobial resistance is a major concern for the dairy industry worldwide. Objectives were to determine: (1) phenotypic and genotypic prevalence of drug-specific resistance for 25 species of non-aureus staphylococci, and (2) associations between presence of resistance determinants and antimicrobial resistance. Broth micro-dilution was used to determine resistance profiles for 1,702 isolates from 89 dairy herds. Additionally, 405 isolates were sequenced to screen for resistance determinants...
2018: Frontiers in Microbiology
Marisa F Nicolás, Pablo Ivan Pereira Ramos, Fabíola Marques de Carvalho, Dhian R A Camargo, Carlene de Fátima Morais Alves, Guilherme Loss de Morais, Luiz G P Almeida, Rangel C Souza, Luciane P Ciapina, Ana C P Vicente, Roney S Coimbra, Ana T Ribeiro de Vasconcelos
The aim of this study was to unravel the genetic determinants responsible for multidrug (including carbapenems) resistance and virulence in a clinical isolate of Klebsiella quasipneumoniae subsp. similipneumoniae by whole-genome sequencing and comparative analyses. Eighty-three clinical isolates initially identified as carbapenem-resistant K. pneumoniae were collected from nosocomial infections in southeast Brazil. After RAPD screening, the KPC-142 isolate, showing the most divergent DNA pattern, was selected for complete genome sequencing in an Illumina HiSeq 2500 instrument...
2018: Frontiers in Microbiology
Dong Wu, Ruoqi Ma, Huawei Wei, Kai Yang, Bing Xie
Around 350 million tons of solid waste is disposed of in landfills every year globally, with millions of cubic meters of landfill leachates released into neighboring environment. However, to date, little is known about the variations of antimicrobial resistance (AMR) in on-site leachate treatment systems and its development in leachate-receiving water environment. Here, we quantified 7 subtypes of antibiotic resistance genes (ARGs), 3 types of culturable antibiotic resistant bacteria (ARB) and 6 subtypes of mobile genetic elements (MGEs) in the effluents from a combined leachate treatment process, including biological treatment (MBR), physical separation (UF), ultraviolet (UV) disinfection and advanced oxidation process (AOP)...
March 1, 2018: Environment International
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