scholarly journals A tale of two plasmids: contributions of plasmid associated phenotypes to epidemiological success among Shigella

2021 ◽  
Author(s):  
P. Malaka De Silva ◽  
George E. Stenhouse ◽  
Grace E. Blackwell ◽  
Rebecca Bengtsson ◽  
Claire Jenkins ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Antimicrobial Resistance ◽  
Horizontal Gene Transfer ◽  
Sos Response ◽  
Transmission Network ◽  
Fitness Costs ◽  
Genomic Epidemiology ◽  
Genes Encoding ◽  
Global Concern ◽  
Epidemiology Studies

Dissemination of antimicrobial resistance (AMR) genes by horizontal gene transfer (HGT) mediated through plasmids is a major global concern. Genomic epidemiology studies have shown varying success of different AMR plasmids during outbreaks, but the underlying reasons for these differences are unclear. Here, we investigated two Shigella plasmids (pKSR100 and pAPR100) that circulated in the same transmission network but had starkly contrasting epidemiological outcomes to identify plasmid features that may have contributed to the differences. We used plasmid comparative genomics to reveal divergence between the two plasmids in genes encoding AMR, SOS response alleviation, and conjugation. Experimental analyses revealed that these genomic differences corresponded with reduced conjugation rates for the epidemiologically successful pKSR100, but more extensive AMR, reduced fitness costs, and a reduced SOS response in the presence of antimicrobials, compared with the less successful pAPR100. The discrepant phenotypes between the two plasmids are consistent with the hypothesis that plasmid associated phenotypes contribute to determining the epidemiological outcome of AMR HGT and suggest that phenotypes relevant in responding to antimicrobial pressure and fitness impact may be more important than those around conjugation in this setting. Plasmid phenotypes could thus be valuable tools in conjunction with genomic epidemiology for predicting AMR dissemination.

scholarly journals Genomic surveillance of Neisseria gonorrhoeae in the Philippines, 2013–2014

2021 ◽  
Vol 12 (1) ◽  
pp. 17-25
Author(s):  
Alfred Villamin ◽  
Silvia Argimon ◽  
Karis Bohme ◽  
Melissa Masim ◽  
June Gayeta ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Neisseria Gonorrhoeae ◽  
Sequence Data ◽  
The Philippines ◽  
Sequence Type ◽  
Surveillance Program ◽  
Gyra Gene ◽  
Genotypic Resistance ◽  
Genomic Epidemiology ◽  
Epidemiology Studies

Antimicrobial-resistant Neisseria gonorrhoeae is a major threat to public health and is of particular concern in the Western Pacific Region, where the incidence of gonorrhoea is high. The Antimicrobial Resistance Surveillance Program (ARSP) has been capturing information on resistant gonorrhoea since 1996, but genomic epidemiology studies on this pathogen are lacking in the Philippines. We sequenced the whole genomes of 21 N. gonorrhoeae isolates collected in 2013–2014 by ARSP. The multilocus sequence type, multiantigen sequence type, presence of determinants of antimicrobial resistance and relatedness among the isolates were all derived from the sequence data. The concordance between phenotypic and genotypic resistance was also determined. Ten of 21 isolates were resistant to penicillin, ciprofloxacin and tetracycline, due mainly to the presence of the blaTEM gene, the S91F mutation in the gyrA gene and the tetM gene, respectively. None of the isolates was resistant to ceftriaxone or cefixime. The concordance between phenotypic and genotypic resistance was 92.38% overall for five antibiotics in four classes. Despite the small number of isolates studied, they were genetically diverse, as shown by the sequence types, the N. gonorrhoeae multiantigen sequence typing types and the tree. Comparison with global genomes placed the Philippine genomes within global lineage A and led to the identification of an international transmission route.

scholarly journals Differences in antimicrobial resistance of Salmonella spp. isolated from humans, animals and food products in Kazakhstan

2021 ◽  
Vol 72 (3) ◽  
pp. 3091
Author(s):  
R RYCHSHANOVA ◽  
M RUZAUSKAS ◽  
G CHUZHEBAYEVA ◽  
R MOCKELIUNAS ◽  
N MAMIYEV ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Horizontal Gene Transfer ◽  
Animal Species ◽  
Food Products ◽  
Poultry Meat ◽  
Genetic Determinants ◽  
Salmonella Spp ◽  
Genes Encoding ◽  
Raw Poultry ◽  
Different Sources

The aims of this study were twofold: 1. to isolate Salmonella spp. from different sources in Kazakhstan, to determine their serovars and resistance profiles and 2. to evaluate similarities in antimicrobial susceptibility of Salmonella spp. isolated from humans, animals and food products. From the10 212 samples tested Salmonella spp. Were isolated in 47 cases. The predominant serovar isolated from humans and food products was S. Enteritidis. Although different animal species were tested the Salmonella spp. were isolated mainly from chickens and ducks. S. Enteritidis and S. Typhimurium were the most prevalent serovars in raw poultry meat. The most frequent resistances were those to nalidixic acid, ampicillin and tetracycline. Human isolates demonstrated lower resistance compared to animal and food isolates. The genes encoding antimicrobial resistance in human isolates in most cases were absent except for some isolates which harboured tet, sul, stre and bla TEM genes encoding resistance to the oldest antimicrobial classes. The situation in animals and food products was less beneficial as besides different genes, integrons associated with the horizontal gene transfer were detected. The findings suggest that antimicrobials in animal sector should be used more strictly, paying attention to critically important antimicrobials for humans and possible horizontal transfer of pathogens and their genetic determinants.

scholarly journals Phylogenomic Insights into Distribution and Adaptation of Bdellovibrionota in Marine Waters

2021 ◽  
Vol 9 (4) ◽  
pp. 757
Author(s):  
Qing-Mei Li ◽  
Ying-Li Zhou ◽  
Zhan-Fei Wei ◽  
Yong Wang
Keyword(s):  
Comparative Genomics ◽  
Deep Sea ◽  
Binding Protein ◽  
Glycerol Metabolism ◽  
Metabolic Reconstruction ◽  
Type Ii Secretion ◽  
Phylogenetic Groups ◽  
Genes Encoding ◽  
Epipelagic Zone ◽  
Chitin Binding Protein

Bdellovibrionota is composed of obligate predators that can consume some Gram-negative bacteria inhabiting various environments. However, whether genomic traits influence their distribution and marine adaptation remains to be answered. In this study, we performed phylogenomics and comparative genomics studies using 132 Bdellovibrionota genomes along with five metagenome-assembled genomes (MAGs) from deep sea zones. Four phylogenetic groups, Oligoflexia, Bdello-group1, Bdello-group2 and Bacteriovoracia, were revealed by constructing a phylogenetic tree, of which 53.84% of Bdello-group2 and 48.94% of Bacteriovoracia were derived from the ocean. Bacteriovoracia was more prevalent in deep sea zones, whereas Bdello-group2 was largely distributed in the epipelagic zone. Metabolic reconstruction indicated that genes involved in chemotaxis, flagellar (mobility), type II secretion system, ATP-binding cassette (ABC) transporters and penicillin-binding protein were necessary for the predatory lifestyle of Bdellovibrionota. Genes involved in glycerol metabolism, hydrogen peroxide (H2O2) degradation, cell wall recycling and peptide utilization were ubiquitously present in Bdellovibrionota genomes. Comparative genomics between marine and non-marine Bdellovibrionota demonstrated that betaine as an osmoprotectant is probably widely used by marine Bdellovibrionota, and all the marine genomes have a number of genes for adaptation to marine environments. The genes encoding chitinase and chitin-binding protein were identified for the first time in Oligoflexia, which implied that Oligoflexia may prey on a wider spectrum of microbes. This study expands our knowledge on adaption strategies of Bdellovibrionota inhabiting deep seas and the potential usage of Oligoflexia for biological control.

scholarly journals Molecular investigation of an outbreak associated with total parenteral nutrition contaminated with NDM-producing Leclercia adecarboxylata

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Elvira Garza-González ◽  
Paola Bocanegra-Ibarias ◽  
Eduardo Rodríguez-Noriega ◽  
Esteban González-Díaz ◽  
Jesús Silva-Sanchez ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Carbapenem Resistance ◽  
Clonal Diversity ◽  
Molecular Characteristics ◽  
Molecular Evidence ◽  
Carbapenem Resistant ◽  
Parental Nutrition ◽  
Genes Encoding ◽  
Main Lineage ◽  
Encoding Genes

Abstract Background This study aimed to determine the epidemiological, microbiological, and molecular characteristics of an outbreak of carbapenem-resistant Leclercia adecarboxylata in three hospitals associated with the unintended use of contaminated total parental nutrition (TPN). Methods For 10 days, 25 patients who received intravenous TPN from the same batch of a formula developed sepsis and had blood cultures positive for L. adecarboxylata. Antimicrobial susceptibility and carbapenemase production were performed in 31 isolates, including one from an unopened bottle of TPN. Carbapenemase-encoding genes, extended-spectrum β-lactamase–encoding genes were screened by PCR, and plasmid profiles were determined. Horizontal transfer of carbapenem resistance was performed by solid mating. Clonal diversity was performed by pulsed-field gel electrophoresis. The resistome was explored by whole-genome sequencing on two selected strains, and comparative genomics was performed using Roary. Results All 31 isolates were resistant to aztreonam, cephalosporins, carbapenems, trimethoprim/sulfamethoxazole, and susceptible to gentamicin, tetracycline, and colistin. Lower susceptibility to levofloxacin (51.6%) and ciprofloxacin (22.6%) was observed. All the isolates were carbapenemase producers and positive for blaNDM-1, blaTEM-1B, and blaSHV-12 genes. One main lineage was detected (clone A, 83.9%; A1, 12.9%; A2, 3.2%). The blaNDM-1 gene is embedded in a Tn125-like element. Genome analysis showed genes encoding resistance for aminoglycosides, quinolones, trimethoprim, colistin, phenicols, and sulphonamides and the presence of IncFII (Yp), IncHI2, and IncHI2A incompatibility groups. Comparative genomics showed a major phylogenetic relationship among L. adecarboxylata I1 and USDA-ARS-USMARC-60222 genomes, followed by our two selected strains. Conclusion We present epidemiological, microbiological, and molecular evidence of an outbreak of carbapenem-resistant L. adecarboxylata in three hospitals in western Mexico associated with the use of contaminated TPN.

scholarly journals A Cotransformation Method To Identify a Restriction-Modification Enzyme That Reduces Conjugation Efficiency inCampylobacter jejuni

2018 ◽  
Vol 84 (23) ◽  
Author(s):  
Ximin Zeng ◽  
Zuowei Wu ◽  
Qijing Zhang ◽  
Jun Lin
Keyword(s):  
Comparative Genomics ◽  
Heat Shock ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Campylobacter Jejuni ◽  
Selection Marker ◽  
Sequencing Analysis ◽  
Content Type ◽  
Restriction Modification ◽  
Modification Enzyme

ABSTRACTConjugation is an important mechanism for horizontal gene transfer inCampylobacter jejuni, the leading cause of human bacterial gastroenteritis in developed countries. However, to date, the factors that significantly influence conjugation efficiency inCampylobacterspp. are still largely unknown. Given that multiple recombinant loci could independently occur within one recipient cell during natural transformation, the genetic materials from a high-frequency conjugation (HFC)C. jejunistrain may be cotransformed with a selection marker into a low-frequency conjugation (LFC) recipient strain, creating new HFC transformants suitable for the identification of conjugation factors using a comparative genomics approach. To test this, an erythromycin resistance selection marker was created in an HFCC. jejunistrain; subsequently, the DNA of this strain was naturally transformed into NCTC 11168, an LFCC. jejunistrain, leading to the isolation of NCTC 11168-derived HFC transformants. Whole-genome sequencing analysis and subsequent site-directed mutagenesis identified Cj1051c, a putative restriction-modification enzyme (akaCjeI) that could drastically reduce the conjugation efficiency of NCTC 11168 (>5,000-fold). Chromosomal complementation of three diverse HFCC. jejunistrains with CjeI also led to a dramatic reduction in conjugation efficiency (∼1,000-fold). The purified recombinant CjeI could effectively digest theEscherichia coli-derived shuttle vector pRY107. The endonuclease activity of CjeI was abolished upon short heat shock treatment at 50°C, which is consistent with our previous observation that heat shock enhanced conjugation efficiency inC. jejuni. Together, in this study, we successfully developed and utilized a unique cotransformation strategy to identify a restriction-modification enzyme that significantly influences conjugation efficiency inC. jejuni.IMPORTANCEConjugation is an important horizontal gene transfer mechanism contributing to the evolution of bacterial pathogenesis and antimicrobial resistance.Campylobacter jejuni, the leading foodborne bacterial organism, displays significant strain diversity due to horizontal gene transfer; however, the molecular components influencing conjugation efficiency inC. jejuniare still largely unknown. In this study, we developed a cotransformation strategy for comparative genomics analysis and successfully identified a restriction-modification enzyme that significantly influences conjugation efficiency inC. jejuni. The new cotransformation strategy developed in this study is also expected to be broadly applied in other naturally competent bacteria for functional comparative genomics research.

scholarly journals Non-Penicillin-Susceptible Streptococcus suis Isolated from Humans

Pathogens ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1178
Author(s):  
Nichari Bamphensin ◽  
Peechanika Chopjitt ◽  
Rujirat Hatrongjit ◽  
Parichart Boueroy ◽  
Nahuel Fittipaldi ◽  
...  
Keyword(s):  
Amino Acid ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Streptococcus Suis ◽  
Amino Acid Substitutions ◽  
Continuous Control ◽  
Antimicrobial Resistance Genes ◽  
Genes Encoding ◽  
Invasive Infections ◽  
Almost All

Streptococcus suis is a pathogen that causes invasive infections in humans and pigs. In this study, 448 S. suis isolates recovered from human infections in Thailand were characterized with regard to their antimicrobial susceptibility and antimicrobial resistance genes, including, for non-penicillin-susceptible isolates, sequence analyses of five genes encoding penicillin-binding proteins (pbp1a, pbp1b, pbp2a, pbp2b, and pbp2x). All 448 isolates were susceptible to cefepime and ceftriaxone, whereas 99.6%, 91.7%, and 72.9% of the isolates were susceptible to levofloxacin, penicillin, and chloramphenicol, respectively. Almost all isolates were resistant to tetracycline (98.2%), clindamycin (94%), erythromycin (92.4%), and azithromycin (82.6%). Genes tet(O) and ermB were the predominant resistance genes detected among macrolide- and tetracycline-resistant isolates. A total of 37 out of 448 isolates (8.2%) showed intermediately resistance to penicillin. Most of these isolates (59.5%) belonged to serotype 2-ST233. Comparison of the predicted translated sequences of five PBP proteins of a penicillin-susceptible isolate (strain P1/7) to the respective PBP sequences of ten non-penicillin-susceptible isolates revealed multiple amino acid substitutions. Isolates of CC221/234 showed highly variable amino acid substitutions in all PBP proteins. An ST104 isolate had a higher number of amino acid substitutions in PBP2X. Isolates belonging to CC233/379 had numerous substitutions in PBP2B and PBP2X. ST25 isolates exhibited fewer amino acid substitutions than isolates of other STs in all five PBPs. The antimicrobial resistance of S. suis is increasing worldwide; therefore, restrictions on antimicrobial use, continuous control, and the surveillance of this bacterium throughout the pork supply chain are crucial for ensuring public health and must be a priority concern.

scholarly journals The face of hypervirulent Klebsiella pneumoniae isolated from clinical samples of two Iranian teaching hospitals

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Rahimeh Sanikhani ◽  
Mohammad Moeinirad ◽  
Hamid Solgi ◽  
Azar Hadadi ◽  
Fereshteh Shahcheraghi ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Antimicrobial Resistance ◽  
Klebsiella Pneumoniae ◽  
High Resistance ◽  
Multidrug Resistant ◽  
Teaching Hospitals ◽  
Clinical Samples ◽  
Clonal Relatedness ◽  
The Face ◽  
Global Concern

AbstractHypervirulent Klebsiella pneumoniae (hvKp) has emerged as a pathogen of global concern. In this study, both phenotypic and genotypic tests were used to detect hvKp. Antimicrobial resistance profiles and clonal relatedness of clinical isolates were also determined. We found that 34.2% (163/477) of the isolates were tellurite resistant, and among them 102 hvKp isolates detected with iucA or iutA or peg-344 as molecular markers. The blaSHV (80.4%), followed by blaCTX-M-15 (76.5%) and blaTEM (67.6%), blaOXA-48 (53.9%), and blaNDM-1 (32.3%) were detected, while blaKPC-1 was not present in any hvKp isolates. It was found that the majority of hvKp isolates belonged to capsular serotype K20 and ompK36 group C, which is related to clonal group (CG) 23 (e.g. ST23). A high percentage of multidrug-resistant hvKp (76.6%) and high resistance to imipenem (67%) indicated a serious problem that should be addressed in the clinical setting.

scholarly journals Genomic variant identification methods alter Mycobacterium tuberculosis transmission inference

2019 ◽  
Author(s):  
Katharine S. Walter ◽  
Caroline Colijn ◽  
Ted Cohen ◽  
Barun Mathema ◽  
Qingyun Liu ◽  
...  
Keyword(s):  
Sequence Data ◽  
Variant Calling ◽  
Genomic Variation ◽  
Human Pathogens ◽  
Phylogenetic Structure ◽  
Genomic Epidemiology ◽  
Tuberculosis Transmission ◽  
Epidemiology Studies ◽  
Global And Local ◽  
Variant Identification

AbstractPathogen genomic data are increasingly used to characterize global and local transmission patterns of important human pathogens and to inform public health interventions. Yet there is no current consensus on how to measure genomic variation. We investigated the effects of variant identification approaches on transmission inferences for M. tuberculosis by comparing variants identified by five different groups in the same sequence data from a clonal outbreak. We then measured the performance of commonly used variant calling approaches in recovering variation in a simulated tuberculosis outbreak and tested the effect of applying increasingly stringent filters on transmission inferences and phylogenies. We found that variant calling approaches used by different groups do not recover consistent sets of variants, often leading to conflicting transmission inferences. Further, performance in recovering true outbreak variation varied widely across approaches. Finally, stringent filters rapidly eroded the accuracy of transmission inferences and quality of phylogenies reconstructed from outbreak variation. We conclude that measurements of genetic distance and phylogenetic structure are dependent on variant calling approach. Variant calling algorithms trained upon true sequence data outperform other approaches and enable inclusion of repetitive regions typically excluded from genomic epidemiology studies, maximizing the information gleaned from outbreak genomes.

scholarly journals Zoonotic Significance and Antimicrobial Resistance in Salmonella in Poultry in Bangladesh for the Period of 2011–2021

2021 ◽  
Vol 1 (1) ◽  
pp. 3-24
Author(s):  
Md. Jannat Hossain ◽  
Youssef Attia ◽  
Fatimah Muhammad Ballah ◽  
Md. Saiful Islam ◽  
Md. Abdus Sobur ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Antimicrobial Resistance ◽  
Horizontal Gene Transfer ◽  
Selection Pressure ◽  
Economic Loss ◽  
Multidrug Resistant ◽  
Foodborne Illness ◽  
The Status ◽  
Resistance Patterns ◽  
Effective Drugs

Antimicrobial resistance (AMR) in Salmonella in poultry poses a serious human health threat as it has zoonotic importance. Poultry is often linked with outbreaks of Salmonella-associated foodborne illness. Since antimicrobials are heavily used in poultry in Bangladesh, multidrug-resistant (MDR) Salmonella is quite frequently found there. MDR Salmonella is challenging to treat with antimicrobials and often causes a severe economic loss in the poultry sector. By horizontal gene transfer and/or evolutionary mutations, antimicrobials primarily exert selection pressure that contributes to antimicrobials resistance. In addition, resistance patterns can vary with variations in time and space. Without having prior knowledge of resistance patterns, no effective drugs could be prescribed. Therefore, it is crucial to have updated knowledge on the status of AMR in Salmonella in Bangladesh for effective treatment and management of the flocks against salmonellosis. There are several review articles on AMR in Salmonella in poultry in Bangladesh; they lack the whole scenario of the country and particularly do not have enough data on the poultry environment. Considering this scenario, in this review, we have focused on AMR in Salmonella in poultry in Bangladesh (2011–2021), with particular emphasis on data from the poultry and farm environments on a divisional zone basis.

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