mSphere of Influence: a Controlled Burn—Pathogen Manipulation of the Dynamic Chemistry That Results from Inflammation

ABSTRACT Neal Hammer works in the field of bacterial pathogenesis, metabolism, and antibiotic resistance. In this mSphere of Influence article, he reflects on how “Gut inflammation provides a respiratory electron acceptor for Salmonella” by Winter and colleagues (S. E. Winter, P. Thiennimitr, M. G. Winter, B. P. Butler, et al., Nature 467:426–429, 2010, https://doi.org/10.1038/nature09415) made an impact on him by demonstrating that Salmonella enterica serotype Typhimurium metabolism is uniquely suited to exploit the chemical by-products that result from the host’s inflammatory response.

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Magnetovibrio blakemorei gen. nov., sp. nov., a magnetotactic bacterium ( Alphaproteobacteria : Rhodospirillaceae ) isolated from a salt marsh

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.044453-0 ◽

2013 ◽

Vol 63 (Pt_5) ◽

pp. 1824-1833 ◽

Cited By ~ 52

Author(s):

Dennis A. Bazylinski ◽

Timothy J. Williams ◽

Christopher T. Lefèvre ◽

Denis Trubitsyn ◽

Jiasong Fang ◽

...

Keyword(s):

Salt Marsh ◽

Electron Acceptor ◽

Anaerobic Growth ◽

Rrna Gene ◽

Magnetotactic Bacterium ◽

Single Chain ◽

Circular Chromosome ◽

Terminal Electron Acceptor ◽

Content Type ◽

Link Type

A magnetotactic bacterium, designated strain MV-1T, was isolated from sulfide-rich sediments in a salt marsh near Boston, MA, USA. Cells of strain MV-1T were Gram-negative, and vibrioid to helicoid in morphology. Cells were motile by means of a single polar flagellum. The cells appeared to display a transitional state between axial and polar magnetotaxis: cells swam in both directions, but generally had longer excursions in one direction than the other. Cells possessed a single chain of magnetosomes containing truncated hexaoctahedral crystals of magnetite, positioned along the long axis of the cell. Strain MV-1T was a microaerophile that was also capable of anaerobic growth on some nitrogen oxides. Salinities greater than 10 % seawater were required for growth. Strain MV-1T exhibited chemolithoautotrophic growth on thiosulfate and sulfide with oxygen as the terminal electron acceptor (microaerobic growth) and on thiosulfate using nitrous oxide (N2O) as the terminal electron acceptor (anaerobic growth). Chemo-organoautotrophic and methylotrophic growth was supported by formate under microaerobic conditions. Autotrophic growth occurred via the Calvin–Benson–Bassham cycle. Chemo-organoheterotrophic growth was supported by various organic acids and amino acids, under microaerobic and anaerobic conditions. Optimal growth occurred at pH 7.0 and 26–28 °C. The genome of strain MV-1T consisted of a single, circular chromosome, about 3.7 Mb in size, with a G+C content of 52.9–53.5 mol%.Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MV-1T belongs to the family Rhodospirillaceae within the Alphaproteobacteria , but is not closely related to the genus Magnetospirillum . The name Magnetovibrio blakemorei gen. nov., sp. nov. is proposed for strain MV-1T. The type strain of Magnetovibrio blakemorei is MV-1T ( = ATCC BAA-1436T = DSM 18854T).

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Alterations of Salmonella enterica Serovar Typhimurium Antibiotic Resistance under Environmental Pressure

Applied and Environmental Microbiology ◽

10.1128/aem.01173-18 ◽

2018 ◽

Vol 84 (19) ◽

Cited By ~ 14

Author(s):

Mengfei Peng ◽

Serajus Salaheen ◽

Robert L. Buchanan ◽

Debabrata Biswas

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Salmonella Enterica ◽

Tetracycline Resistance ◽

Multidrug Resistant ◽

Genetic Alterations ◽

Antibiotic Resistant ◽

Content Type ◽

Farm Systems ◽

Serovar Typhimurium

ABSTRACT Microbial horizontal gene transfer is a continuous process that shapes bacterial genomic adaptation to the environment and the composition of concurrent microbial ecology. This includes the potential impact of synthetic antibiotic utilization in farm animal production on overall antibiotic resistance issues; however, the mechanisms behind the evolution of microbial communities are not fully understood. We explored potential mechanisms by experimentally examining the relatedness of phylogenetic inference between multidrug-resistant Salmonella enterica serovar Typhimurium isolates and pathogenic Salmonella Typhimurium strains based on genome-wide single-nucleotide polymorphism (SNP) comparisons. Antibiotic-resistant S. Typhimurium isolates in a simulated farm environment barely lost their resistance, whereas sensitive S. Typhimurium isolates in soils gradually acquired higher tetracycline resistance under antibiotic pressure and manipulated differential expression of antibiotic-resistant genes. The expeditious development of antibiotic resistance and the ensuing genetic alterations in antimicrobial resistance genes in S. Typhimurium warrant effective actions to control the dissemination of Salmonella antibiotic resistance. IMPORTANCE Antibiotic resistance is attributed to the misuse or overuse of antibiotics in agriculture, and antibiotic resistance genes can also be transferred to bacteria under environmental stress. In this study, we report a unidirectional alteration in antibiotic resistance from susceptibility to increased resistance. Highly sensitive Salmonella enterica serovar Typhimurium isolates from organic farm systems quickly acquired tetracycline resistance under antibiotic pressure in simulated farm soil environments within 2 weeks, with expression of antibiotic resistance-related genes that was significantly upregulated. Conversely, originally resistant S. Typhimurium isolates from conventional farm systems lost little of their resistance when transferred to environments without antibiotic pressure. Additionally, multidrug-resistant S. Typhimurium isolates genetically shared relevancy with pathogenic S. Typhimurium isolates, whereas susceptible isolates clustered with nonpathogenic strains. These results provide detailed discussion and explanation about the genetic alterations and simultaneous acquisition of antibiotic resistance in S. Typhimurium in agricultural environments.

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The Invasion Plasmid Antigen J (IpaJ) from Salmonella Inhibits NF-κB Activation by Suppressing IκBα Ubiquitination

Infection and Immunity ◽

10.1128/iai.00875-19 ◽

2019 ◽

Vol 88 (3) ◽

Author(s):

Qiuchun Li ◽

Lijuan Xu ◽

Chao Yin ◽

Zijian Liu ◽

Yang Li ◽

...

Keyword(s):

Inflammatory Response ◽

Proinflammatory Cytokines ◽

Hela Cells ◽

Salmonella Enterica ◽

Systemic Infection ◽

Peripheral Blood Monocyte ◽

Effector Proteins ◽

Economic Losses ◽

Necrosis Factor Alpha ◽

Content Type

ABSTRACT Salmonella enterica serovar Pullorum is the pathogen of pullorum disease, which leads to severe economic losses in many developing countries. In contrast to the strong inflammatory response induced by Salmonella enterica serovar Typhimurium and Salmonella enterica serovar Enteritidis, S. Pullorum causes systemic infection with little inflammation. The effector proteins secreted by Salmonella often play a crucial role in modulating host signal transduction and cellular processes to the pathogen’s advantage. In the present study, the invasion plasmid antigen J (IpaJ) protein specifically identified in S. Pullorum was found to significantly inhibit activation of the key proinflammatory transcription factor, NF-κB, which was induced by tumor necrosis factor alpha (TNF-α), interleukin-1β (IL-1β), and lipopolysaccharide (LPS). IpaJ inhibited the NF-κB pathway in cells infected with S. Pullorum through the stabilization of IκBα. Deletion of ipaJ in S. Pullorum caused a significantly increased level of ubiquitinated IκBα that was subsequently degraded by the proteasome in HeLa cells. Moreover, IpaJ was efficient in the prevention of NF-κB translocation to the nucleus and ultimately interfered with the secretion of the proinflammatory cytokines IL-1β, IL-6, and IL-8 in infected HeLa cells. Additionally, the transformation of ipaJ into S. Enteritidis decreased the secretion of proinflammatory cytokines in HeLa cells through suppression of the NF-κB pathway. The infection of chicken peripheral blood monocyte-derived macrophages (chMDM) confirmed that ipaJ-deleted S. Pullorum induced a stronger expression of proinflammatory cytokines than the wild-type and complementary strains. In summary, the present study revealed that IpaJ functions as an important anti-inflammatory protein involved in S. Pullorum infection through inhibition of the NF-κB pathway and the subsequent inflammatory response.

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Draft Genome Sequences of Ciprofloxacin-Resistant Salmonella enterica Strains with Multiple-Antibiotic Resistance, Isolated from Imported Foods

Genome Announcements ◽

10.1128/genomea.01222-17 ◽

2017 ◽

Vol 5 (45) ◽

Author(s):

Ashraf A. Khan ◽

Bijay K. Khajanchi ◽

Sana A. Khan ◽

Christopher A. Elkins ◽

Steven L. Foley

Keyword(s):

Antibiotic Resistance ◽

Salmonella Enterica ◽

Draft Genome ◽

Resistance Mechanisms ◽

Whole Genome Sequencing Data ◽

Sequencing Data ◽

Genome Sequences ◽

Content Type ◽

Imported Foods ◽

High Level

ABSTRACT We report here the draft genome sequences of 15 ciprofloxacin-resistant Salmonella enterica strains with resistance to multiple other antibiotics, including aminoglycosides, β-lactams, sulfonamides, tetracycline, and trimethoprim, isolated from different imported foods. Three strains (NCTR75, NCTR281, and NCTR350) showed a high level of ciprofloxacin resistance compared to that of the other isolates. The whole-genome sequencing data provide a better understanding of the antibiotic resistance mechanisms and virulence properties of these isolates.

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Elucidation of global and national genomic epidemiology of Salmonella enterica serovar Enteritidis through multilevel genome typing

Microbial Genomics ◽

10.1099/mgen.0.000605 ◽

2021 ◽

Vol 7 (7) ◽

Author(s):

Lijuan Luo ◽

Michael Payne ◽

Sandeep Kaur ◽

Dalong Hu ◽

Liam Cheney ◽

...

Keyword(s):

Salmonella Enterica ◽

Large Scale ◽

Temporal Trends ◽

Rapid Expansion ◽

Outbreak Detection ◽

Content Type ◽

Genomic Epidemiology ◽

Link Type ◽

Promising Tool ◽

Genome Typing

Salmonella enterica serovar Enteritidis is a major cause of foodborne Salmonella infections and outbreaks in humans. Effective surveillance and timely outbreak detection are essential for public health control. Multilevel genome typing (MGT) with multiple levels of resolution has been previously demonstrated as a promising tool for this purpose. In this study, we developed MGT with nine levels for S. Enteritidis and characterised the genomic epidemiology of S. Enteritidis in detail. We examined 26 670 publicly available S. Enteritidis genome sequences from isolates spanning 101 years from 86 countries to reveal their spatial and temporal distributions. Using the lower resolution MGT levels, globally prevalent and regionally restricted sequence types (STs) were identified; avian associated MGT4-STs were found that were common in human cases in the USA; temporal trends were observed in the UK with MGT5-STs from 2014 to 2018 revealing both long lived endemic STs and the rapid expansion of new STs. Using MGT3 to MGT6, we identified multidrug resistance (MDR) associated STs at various MGT levels, which improves precision of detection and global tracking of MDR clones. We also found that the majority of the global S. Enteritidis population fell within two predominant lineages, which had significantly different propensity of causing large scale outbreaks. An online open MGT database has been established for unified international surveillance of S. Enteritidis. We demonstrated that MGT provides a flexible and high-resolution genome typing tool for S. Enteritidis surveillance and outbreak detection.

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Prevalence of Mycoplasma genitalium fluoroquinolone-resistance markers, and dual-class-resistance markers, in asymptomatic men who have sex with men

Journal of Medical Microbiology ◽

10.1099/jmm.0.001429 ◽

2021 ◽

Vol 70 (9) ◽

Author(s):

Teck-Phui Chua ◽

Kaveesha Bodiyabadu ◽

Dorothy A. Machalek ◽

Suzanne M. Garland ◽

Catriona S. Bradshaw ◽

...

Keyword(s):

Antibiotic Resistance ◽

Type Species ◽

Health Centre ◽

Mycoplasma Genitalium ◽

Fluoroquinolone Resistance ◽

Content Type ◽

Link Type ◽

Resistance Markers ◽

Sex With Men ◽

Dual Class

Introduction. Failure of fluoroquinolones, the principal treatment option for macrolide-resistant Mycoplasma genitalium infections, has recently emerged. This is of particular concern for men who have sex with men (MSM), who have high proportions of macrolide-resistant M. genitalium infections. Treatment failure with moxifloxacin is likely the result of single nucleotide polymorphisms (SNPs) in parC, whilst concurrent gyrA mutations may play a role. Gap Statement. The levels of fluoroquinolone resistance and dual-class (i.e. macrolide and fluoroquinolone) resistance in M. genitalium among asymptomatic MSM is unknown. Aim. To (i) determine the proportion of fluoroquinolone resistance and dual-class resistance in M. genitalium infections among asymptomatic MSM, (ii) explore any clinical and behavioural associations with fluoroquinolone resistance, and (iii) determine the distribution of antibiotic resistance among M. genitalium mgpB sequence types (STs). Methodology. M. genitalium positive samples (N=94) were obtained from 1001 asymptomatic MSM enrolled in a study at Melbourne Sexual Health Centre (Carlton, Australia) between August 2016 and September 2017. Sanger sequencing was performed to determine the proportion of M. genitalium infections with SNPs in parC that have previously been associated with failure of moxifloxacin (corresponding to amino changes S83I, D83R, D87Y and D87N) and in gyrA (corresponding to amino acid changes M95I, D99N, D99Y and D99G). Associations between clinical/behavioural factors and parC SNPs were examined. Strain typing was performed by sequencing a portion of the mgpB gene. Results. The proportion of MSM with infections harbouring parC and gyrA SNPs was 13.0 % [95 % confidence interval (CI): 6.8–23.2 %] and 4.7 % (95 % CI: 1.1–13.4 %), respectively; dual-class resistance was 13.0 %. No significant clinical/behavioural associations were found. Antibiotic resistance was not restricted to specific mgpB STs. Conclusion. One in eight (13 %) of asymptomatic MSM with M. genitalium had an infection with dual-class-resistance mutations. Typing by mgpB sequence suggested fluoroquinolone resistance is arising from independent mutation events. This study illustrates that asymptomatic MSM may act as a reservoir for antibiotic-resistant M. genitalium .

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Influence of SOS-inducing agents on the expression of ArtAB toxin gene in Salmonella enterica and Salmonella bongori

Microbiology ◽

10.1099/mic.0.000939 ◽

2020 ◽

Vol 166 (8) ◽

pp. 785-793

Author(s):

Shou Miura ◽

Yukino Tamamura ◽

Mariko Takayasu ◽

Miwa Sasaki ◽

Natsuko Nishimura ◽

...

Keyword(s):

Salmonella Enterica ◽

Type Species ◽

Phage Type ◽

Sos Response ◽

Toxin Gene ◽

Efficient Production ◽

Prophage Induction ◽

Content Type ◽

Link Type ◽

Quinolone Antibiotics

Salmonella enterica subspecies enterica serovar Typhimurium (S. Typhimurium) definitive phage type 104 (DT104), S. enterica subspecies enterica serovar Worthington (S. Worthington) and S. bongori produce ArtA and ArtB (ArtAB) toxin homologues, which catalyse ADP-ribosylation of pertussis toxin-sensitive G protein. ArtAB gene (artAB) is encoded on prophage in DT104 and its expression is induced by mitomycin C (MTC) and hydrogen peroxide (H2O2) that trigger the bacterial SOS response. Although the genetic regulatory mechanism associated with artAB expression is not characterized, it is thought to be associated with prophage induction, which occurs when the RecA-mediated SOS response is triggered. Here we show that subinhibitory concentration of quinolone antibiotics that are SOS-inducing agents, also induce ArtAB production in these Salmonella strains. Both MTC and fluoroquinolone antibiotics such as enrofloxacin-induced artA and recA transcription and artAB-encoding prophage (ArtAB-prophage) in DT104 and S. Worthington. However, in S. bongori , which harbours artAB genes on incomplete prophage, artA transcription was induced by MTC and enrofloxacin, but prophage induction was not observed. Taken together, these results suggest that SOS response followed by induction of artAB transcription is essential for ArtAB production. H2O2-mediated induction of ArtAB prophage and efficient production of ArtAB was observed in DT104 but not in S. Worthington and S. bongori . Therefore, induction of artAB expression with H2O2 is strain-specific, and the mode of action of H2O2 as an SOS-inducing agent might be different from those of MTC and quinolone antibiotics.

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bla OXA-48-like genome architecture among carbapenemase-producing Escherichia coli and Klebsiella pneumoniae in the Netherlands

Microbial Genomics ◽

10.1099/mgen.0.000512 ◽

2021 ◽

Vol 7 (5) ◽

Author(s):

Antoni P. A. Hendrickx ◽

Fabian Landman ◽

Angela de Haan ◽

Sandra Witteveen ◽

Marga G. van Santen-Verheuvel ◽

...

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

The Netherlands ◽

Resistance Genes ◽

Type Species ◽

Antibiotic Resistance Genes ◽

Gene Content ◽

Content Type ◽

E Coli ◽

Link Type

Carbapenem-hydrolysing enzymes belonging to the OXA-48-like group are encoded by bla OXA-48-like alleles and are abundant among Enterobacterales in the Netherlands. Therefore, the objective here was to investigate the characteristics, gene content and diversity of the bla OXA-48-like carrying plasmids and chromosomes of Escherichia coli and Klebsiella pneumoniae collected in the Dutch national surveillance from 2014 to 2019 in comparison with genome sequences from 29 countries. A combination of short-read genome sequencing with long-read sequencing enabled the reconstruction of 47 and 132 complete bla OXA-48-like plasmids for E. coli and K. pneumoniae , respectively. Seven distinct plasmid groups designated as pOXA-48-1 to pOXA-48-5, pOXA-181 and pOXA-232 were identified in the Netherlands which were similar to internationally reported plasmids obtained from countries from North and South America, Europe, Asia and Oceania. The seven plasmid groups varied in size, G+C content, presence of antibiotic resistance genes, replicon family and gene content. The pOXA-48-1 to pOXA-48-5 plasmids were variable, and the pOXA-181 and pOXA-232 plasmids were conserved. The pOXA-48-1, pOXA-48-2, pOXA-48-3 and pOXA-48-5 groups contained a putative conjugation system, but this was absent in the pOXA-48-4, pOXA-181 and pOXA-232 plasmid groups. pOXA-48 plasmids contained the PemI antitoxin, while the pOXA-181 and pOXA-232 plasmids did not. Furthermore, the pOXA-181 plasmids carried a virB2-virB3-virB9-virB10-virB11 type IV secretion system, while the pOXA-48 plasmids and pOXA-232 lacked this system. A group of non-related pOXA-48 plasmids from the Netherlands contained different resistance genes, non-IncL-type replicons or no replicons. Whole genome multilocus sequence typing revealed that the bla OXA-48-like plasmids were found in a wide variety of genetic backgrounds in contrast to chromosomally encoded bla OXA-48-like alleles. Chromosomally localized bla OXA-48 and bla OXA-244 alleles were located on genetic elements of variable sizes and comprised regions of pOXA-48 plasmids. The bla OXA-48-like genetic element was flanked by a direct repeat upstream of IS1R, and was found at multiple locations in the chromosomes of E. coli . Lastly, K. pneumoniae isolates carrying bla OXA-48 or bla OXA-232 were mostly resistant for meropenem, whereas E. coli bla OXA-48, bla OXA-181 and chromosomal bla OXA-48 or bla OXA-244 isolates were mostly sensitive. In conclusion, the overall bla OXA-48-like plasmid population in the Netherlands is conserved and similar to that reported for other countries, confirming global dissemination of bla OXA-48-like plasmids. Variations in size, presence of antibiotic resistance genes and gene content impacted pOXA-48, pOXA-181 and pOXA-232 plasmid architecture.

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Phylum barrier and Escherichia coli intra-species phylogeny drive the acquisition of antibiotic-resistance genes

Microbial Genomics ◽

10.1099/mgen.0.000489 ◽

2021 ◽

Vol 7 (8) ◽

Author(s):

Marie Petitjean ◽

Bénédicte Condamine ◽

Charles Burdet ◽

Erick Denamur ◽

Etienne Ruppé

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

Resistance Genes ◽

Type Species ◽

Antibiotic Resistance Genes ◽

Resistance Pattern ◽

Content Type ◽

E Coli ◽

Link Type ◽

Specific Distribution

Escherichia coli is a ubiquitous bacterium that has been widely exposed to antibiotics over the last 70 years. It has adapted by acquiring different antibiotic-resistance genes (ARGs), the census of which we aim to characterize here. To do so, we analysed 70 301 E. coli genomes obtained from the EnteroBase database and detected 1 027 651 ARGs using the AMRFinder, Mustard and ResfinderFG ARG databases. We observed a strong phylogroup and clonal lineage specific distribution of some ARGs, supporting the argument for epistasis between ARGs and the strain genetic background. However, each phylogroup had ARGs conferring a similar antibiotic class resistance pattern, indicating phenotypic adaptive convergence. The G+C content or the type of ARG was not associated with the frequency of the ARG in the database. In addition, we identified ARGs from anaerobic, non- Proteobacteria bacteria in four genomes of E. coli , supporting the hypothesis that the transfer between anaerobic bacteria and E. coli can spontaneously occur but remains exceptional. In conclusion, we showed that phylum barrier and intra-species phylogenetic history are major drivers of the acquisition of a resistome in E. coli .

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Complete Genome Sequence of Salmonella enterica subsp. enterica Serovar Kottbus Strain Kharkiv, Isolated from a Commercial Pork Production Facility in Ukraine

Microbiology Resource Announcements ◽

10.1128/mra.01171-20 ◽

2020 ◽

Vol 9 (49) ◽

Author(s):

Vasiliy Arefiev ◽

Ganna Kovalenko ◽

Maciej Frant ◽

Tetiana Chumachenko ◽

Yuliia Polyvianna ◽

...

Keyword(s):

Antibiotic Resistance ◽

Genome Sequence ◽

Complete Genome Sequence ◽

Salmonella Enterica ◽

Complete Genome ◽

Human Infection ◽

Production Facility ◽

Content Type ◽

Pork Production ◽

Long Read

ABSTRACT The complete genome of Salmonella enterica subsp. enterica serovar Kottbus strain Kharkiv (serogroup C2-C3), which was isolated from a commercial pork production facility in Kharkiv, Ukraine, was assembled using long-read Nanopore sequences. A single circular contig (4,799,045 bp) comprised a complete chromosome encoding antibiotic resistance, highlighting the risk of cross-species livestock and human infection.

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