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Fulltext Heavy-metal resistance of a France vineyard soil bacterium, Pseudomonas mendocina strain S5.2, revealed by whole-genome sequencing

Chong TM, Yin WF, Mondy S, Grandclément C, Dessaux Y, Chan KG

J Bacteriol, 2012 Nov;194(22):6366.
PMID: 23105092 DOI: 10.1128/JB.01702-12

Here we present the draft genome of Pseudomonas mendocina strain S5.2, possessing tolerance to a high concentration of copper. In addition to being copper resistant, the genome of P. mendocina strain S5.2 contains a number of heavy-metal-resistant genes known to confer resistance to multiple heavy-metal ions.

Matched MeSH terms: Genome, Bacterial*
Fulltext Global genome comparative analysis reveals insights of resistome and life-style adaptation of Pseudomonas putida strain T2-2 in oral cavity

Chan XY, Chua KO, How KY, Yin WF, Chan KG

ScientificWorldJournal, 2014;2014:930727.
PMID: 25436236 DOI: 10.1155/2014/930727

Most Pseudomonas putida strains are environmental microorganisms exhibiting a wide range of metabolic capability but certain strains have been reported as rare opportunistic pathogens and some emerged as multidrug resistant P. putida. This study aimed to assess the drug resistance profile of, via whole genome analysis, P. putida strain T2-2 isolated from oral cavity. At the same time, we also compared the nonenvironmental strain with environmentally isolated P. putida. In silico comparative genome analysis with available reference strains of P. putida shows that T2-2 has lesser gene counts on carbohydrate and aromatic compounds metabolisms, which suggested its little versatility. The detection of its edd gene also suggested T2-2's catabolism of glucose via ED pathway instead of EMP pathway. On the other hand, its drug resistance profile was observed via in silico gene prediction and most of the genes found were in agreement with drug-susceptibility testing in laboratory by automated VITEK 2. In addition, the finding of putative genes of multidrug resistance efflux pump and ATP-binding cassette transporters in this strain suggests a multidrug resistant phenotype. In summary, it is believed that multiple metabolic characteristics and drug resistance in P. putida strain T2-2 helped in its survival in human oral cavity.

Matched MeSH terms: Genome, Bacterial/genetics*
Fulltext Genomic reconnaissance of clinical isolates of emerging human pathogen Mycobacterium abscessus reveals high evolutionary potential

Choo SW, Wee WY, Ngeow YF, Mitchell W, Tan JL, Wong GJ, et al.

Sci Rep, 2014;4:4061.
PMID: 24515248 DOI: 10.1038/srep04061

Mycobacterium abscessus (Ma) is an emerging human pathogen that causes both soft tissue infections and systemic disease. We present the first comparative whole-genome study of Ma strains isolated from patients of wide geographical origin. We found a high proportion of accessory strain-specific genes indicating an open, non-conservative pan-genome structure, and clear evidence of rapid phage-mediated evolution. Although we found fewer virulence factors in Ma compared to M. tuberculosis, our data indicated that Ma evolves rapidly and therefore should be monitored closely for the acquisition of more pathogenic traits. This comparative study provides a better understanding of Ma and forms the basis for future functional work on this important pathogen.

Matched MeSH terms: Genome, Bacterial*
Genomic plasticity between human and mycobacterial DNA: A review

Danjuma L, Ling MP, Hamat RA, Higuchi A, Alarfaj AA, Marlina, et al.

Tuberculosis (Edinb), 2017 12;107:38-47.
PMID: 29050770 DOI: 10.1016/j.tube.2017.03.006

Mycobacterium tuberculosis has a remarkable ability of long-term persistence despite vigorous host immunity and prolonged therapy. The bacteria persist in secure niches such as the mesenchymal stem cells in the bone marrow and reactivate the disease, leading to therapeutic failure. Many bacterial cells can remain latent within a diseased tissue so that their genetic material can be incorporated into the genetic material of the host tissue. This incorporated genetic material reproduces in a manner similar to that of cellular DNA. After the cell division, the incorporated gene is reproduced normally and distributed proportionately between the two progeny. This inherent adoption of long-term persistence and incorporating the bacterial genetic material into that of the host tissue remains and is considered imperative for microbial advancement and chemotherapeutic resistance; moreover, new evidence indicates that the bacteria might pass on genetic material to the host DNA sequence. Several studies focused on the survival mechanism of M. tuberculosis in the host immune system with the aim of helping the efforts to discover new drugs and vaccines against tuberculosis. This review explored the mechanisms through which this bacterium affects the expression of human genes. The first part of the review summarizes the current knowledge about the interactions between microbes and host microenvironment, with special reference to the M. tuberculosis neglected persistence in immune cells and stem cells. Then, we focused on how bacteria can affect human genes and their expression. Furthermore, we analyzed the literature base on the process of cell death during tuberculosis infection, giving particular emphasis to gene methylation as an inherited process in the neutralization of possibly injurious gene components in the genome. The final section discusses recent advances related to the M. tuberculosis interaction with host epigenetic circuitry.

Matched MeSH terms: Genome, Bacterial*
Fulltext Genomic epidemiology of tuberculosis in eastern Malaysia: insights for strengthening public health responses

Bainomugisa A, Meumann EM, Rajahram GS, Ong RT, Coin L, Paul DC, et al.

Microb Genom, 2021 05;7(5).
PMID: 33945455 DOI: 10.1099/mgen.0.000573

Tuberculosis is a leading public health priority in eastern Malaysia. Knowledge of the genomic epidemiology of tuberculosis can help tailor public health interventions. Our aims were to determine tuberculosis genomic epidemiology and characterize resistance mutations in the ethnically diverse city of Kota Kinabalu, Sabah, located at the nexus of Malaysia, Indonesia, Philippines and Brunei. We used an archive of prospectively collected Mycobacterium tuberculosis samples paired with epidemiological data. We collected sputum and demographic data from consecutive consenting outpatients with pulmonary tuberculosis at the largest tuberculosis clinic from 2012 to 2014, and selected samples from tuberculosis inpatients from the tertiary referral centre during 2012-2014 and 2016-2017. Two hundred and eight M. tuberculosis sequences were available for analysis, representing 8 % of cases notified during the study periods. Whole-genome phylogenetic analysis demonstrated that most strains were lineage 1 (195/208, 93.8 %), with the remainder being lineages 2 (8/208, 3.8 %) or 4 (5/208, 2.4 %). Lineages or sub-lineages were not associated with patient ethnicity. The lineage 1 strains were diverse, with sub-lineage 1.2.1 being dominant (192, 98 %). Lineage 1.2.1.3 isolates were geographically most widely distributed. The greatest diversity occurred in a border town sub-district. The time to the most recent common ancestor for the three major lineage 1.2.1 clades was estimated to be the year 1966 (95 % HPD 1948-1976). An association was found between failure of culture conversion by week 8 of treatment and infection with lineage 2 (4/6, 67 %) compared with lineage 1 strains (4/83, 5 %) (P<0.001), supporting evidence of greater virulence of lineage 2 strains. Eleven potential transmission clusters (SNP difference ≤12) were identified; at least five included people living in different sub-districts. Some linked cases spanned the whole 4-year study period. One cluster involved a multidrug-resistant tuberculosis strain matching a drug-susceptible strain from 3 years earlier. Drug resistance mutations were uncommon, but revealed one phenotype-genotype mismatch in a genotypically multidrug-resistant isolate, and rare nonsense mutations within the katG gene in two isolates. Consistent with the regionally mobile population, M. tuberculosis strains in Kota Kinabalu were diverse, although several lineage 1 strains dominated and were locally well established. Transmission clusters - uncommonly identified, likely attributable to incomplete sampling - showed clustering occurring across the community, not confined to households or sub-districts. The findings indicate that public health priorities should include active case finding and early institution of tuberculosis management in mobile populations, while there is a need to upscale effective contact investigation beyond households to include other contacts within social networks.

Matched MeSH terms: Genome, Bacterial
Genomic and phenomic analysis of a marine bacterium, Photobacterium marinum J15

Roslan NN, Ngalimat MS, Leow ATC, Oslan SN, Baharum SN, Sabri S

Microbiol Res, 2020 Mar;233:126410.
PMID: 31945517 DOI: 10.1016/j.micres.2020.126410

Photobacterium species are widely distributed in the marine environment. The overall metabolism of this genus remains largely unknown. In order to improve our knowledge on this bacterium, the relationship between the genome and phenome of the Photobacterium isolate was analyzed. The cream colored, Gram-negative, rod-shaped and motile bacterial strain, J15, was isolated from marine water of Tanjung Pelepas, Johor, Malaysia. The 5,684,538 bp genome of strain J15 comprised 3 contigs (2 chromosomes and 1 plasmid) with G + C content of 46.39 % and contained 4924 protein-coding genes including 180 tRNAs and 40 rRNAs. The phenotypic microarray (PM) as analyzed using BIOLOG showed the utilization of; i) 93 of the 190 carbon sources tested, where 61 compounds were used efficiently; ii) 41 of the 95 nitrogen sources tested, where 22 compounds were used efficiently; and iii) 3 of the 94 phosphorous and sulphur sources tested. Furthermore, high tolerance to osmotic stress, basic pH and toxic compounds as well as resistance to antibiotics of strain J15 were determined by BIOLOG PM. The ANI and kSNP analyses revealed that strain J15 to be the same species with Photobacterium marinum AK15 with ANI value of 96.93 % and bootstrapping value of 100 in kSNP. Based on the ANI and kSNP analyses, strain J15 was identified as P. marinum J15.

Matched MeSH terms: Genome, Bacterial*
Genomic analysis revealing the resistance mechanisms of extended-spectrum β-lactamase-producing Klebsiella pneumoniae isolated from pig and humans in Malaysia

Mobasseri G, Thong KL, Teh CSJ

Int Microbiol, 2021 May;24(2):243-250.
PMID: 33469786 DOI: 10.1007/s10123-021-00161-5

Extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae has been associated with a wide range of infections in humans and animals. The objective of this study was to determine the genomic characteristics of two multiple drug resistant, ESBLs-producing K. pneumoniae strains isolated from a swine in 2013 (KP2013Z28) and a hospitalized patient in 2014 (KP2014C46) in Malaysia. Genomic analyses of the two K. pneumoniae strains indicated the presence of various antimicrobial resistance genes associated with resistance to β-lactams, aminoglycosides, colistin, fluoroquinolones, phenicols, tetracycline, sulfonamides, and trimethoprim, corresponding to the antimicrobial susceptibility profiles of the strains. KP2013Z28 (ST25) and KP2014C46 (ST929) harbored 5 and 2 genomic plasmids, respectively. The phylogenomics of these two Malaysian K. pneumoniae, with other 19 strains around the world was determined based on SNPs analysis. Overall, the strains were resolved into five clusters that comprised of strains with different resistance determinants. This study provided a better understanding of the resistance mechanisms and phylogenetic relatedness of the Malaysian strains with 19 strains isolated worldwide. This study also highlighted the needs to monitor the usage of antibiotics in hospital settings, animal husbandry, and agricultural practices due to the increase of β-lactam, aminoglycosides, tetracycline, and colistin resistance among pathogenic bacteria for better infection control.

Matched MeSH terms: Genome, Bacterial
Fulltext Genomic analysis of methicillin-resistant Staphylococcus aureus strain SO-1977 from Sudan

Ali MS, Isa NM, Abedelrhman FM, Alyas TB, Mohammed SE, Ahmed AE, et al.

BMC Microbiol, 2019 06 11;19(1):126.
PMID: 31185900 DOI: 10.1186/s12866-019-1470-2

BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA) is known as a leading cause of morbidity and mortality. Investigation of the MRSA's virulence and resistance mechanisms is a continuing concern toward controlling such burdens through using high throughput whole Genome Sequencing (WGS) and molecular diagnostic assays. The objective of the present study is to perform whole-genome sequencing of MRSA isolated from Sudan using Illumina Next Generation Sequencing (NGS) platform.
RESULTS: The genome of MRSA strain SO-1977 consists of 2,827,644 bp with 32.8% G + C, 59 RNAs and 2629 predicted coding sequences (CDSs). The genome has 26 systems, one of which is the major class in the disease virulence and defence. A total of 83 genes were annotated to virulence disease and defence category some of these genes coding as functional proteins. Based on genome analysis, it is speculated that the SO-1977 strain has resistant genes to Teicoplanin, Fluoroquinolones, Quinolone, Cephamycins, Tetracycline, Acriflavin and Carbapenems. The results revealed that the SO-1977, strain isolated from Sudan has a wide range of antibiotic resistance compared to related strains.
CONCLUSION: The study reports for the first time the whole genome sequence of Sudan MRSA isolates. The release of the genome sequence of the strain SO-1977 will avail MRSA in public databases for further investigations on the evolution of resistant mechanism and dissemination of the -resistant genes of MRSA.

Matched MeSH terms: Genome, Bacterial
Genomic analysis of a lignocellulose degrading strain from the underexplored genus Meridianimaribacter

Lam MQ, Oates NC, Thevarajoo S, Tokiman L, Goh KM, McQueen-Mason SJ, et al.

Genomics, 2020 01;112(1):952-960.
PMID: 31201854 DOI: 10.1016/j.ygeno.2019.06.011

The genus Meridianimaribacter is one of the least-studied genera within Cytophaga-Flavobacteria. To date, no genomic analysis of Meridianimaribacter has been reported. In this study, Meridianimaribacter sp. strain CL38, a lignocellulose degrading halophile was isolated from mangrove soil. The genome of strain CL38 was sequenced and analyzed. The assembled genome contains 17 contigs with 3.33 Mbp, a GC content of 33.13% and a total of 2982 genes predicted. Lignocellulose degrading enzymes such as cellulases (GH3, 5, 9, 16, 74 and 144), xylanases (GH43 and CE4) and mannanases (GH5, 26, 27 and 130) are encoded in the genome. Furthermore, strain CL38 demonstrated its ability to decompose empty fruit bunch, a lignocellulosic waste residue arising from palm oil industry. The genome information coupled with experimental studies confirmed the ability of strain CL38 to degrade lignocellulosic biomass. Therefore, Meridianimaribacter sp. strain CL38, with its halotolerance, could be useful for seawater based lignocellulosic biorefining.

Matched MeSH terms: Genome, Bacterial*
Fulltext Genomic analysis of Mycobacterium abscessus strain M139, which has an ambiguous subspecies taxonomic position

Ngeow YF, Wee WY, Wong YL, Tan JL, Ongi CS, Ng KP, et al.

J Bacteriol, 2012 Nov;194(21):6002-3.
PMID: 23045507 DOI: 10.1128/JB.01455-12

Mycobacterium abscessus is a ubiquitous, rapidly growing species of nontuberculous mycobacteria that colonizes organic surfaces and is frequently associated with opportunistic infections in humans. We report here the draft genome sequence of Mycobacterium abscessus strain M139, which shows genomic features reported to be characteristic of both Mycobacterium abscessus subsp. abscessus and Mycobacterium abscessus subsp. massiliense.

Matched MeSH terms: Genome, Bacterial*
Genomic analyses of five Roseivirga species: Insights into marine adaptation

Selvaratnam C, Thevarajoo S, Goh KM, Chan KG, Chong CS

Mar Genomics, 2018 Apr;38:97-101.
PMID: 29306571 DOI: 10.1016/j.margen.2017.12.008

To date, the genus Roseivirga consists of six species with one subspecies and is one of the least-studied genera among the family Flammeovirgaceae. In order to further explore this genus, the genome sequences of five Roseivirga spp. were compared and described in this study. The Roseivirga genomes have similar sizes in the range of 4.08-4.47Mb with an average of 4.22Mb. Several key proteins related to osmotic stress adaptation were identified in Roseivirga spp. including betaine transporter, choline dehydrogenase, and glutamate synthases. Significant amount of proteins associated with amino acid transport and metabolism were also present in Roseivirga genome. All five Roseivirga spp. were able to grow in medium contained casamino acids (mixture of amino acids) as sole carbon or nitrogen sources. Taken together, these findings suggested the potential role of Roseivirga in decomposing organic nitrogen matter in marine environment.

Matched MeSH terms: Genome, Bacterial*
Fulltext Genomic Analysis of Mycobacterium massiliense strain M115, an isolate from human sputum

Ngeow YF, Wong YL, Lokanathan N, Wong GJ, Ong CS, Ng KP, et al.

J Bacteriol, 2012 Sep;194(17):4786.
PMID: 22887681 DOI: 10.1128/JB.01104-12

We report the draft genome sequence of a clinical isolate, strain M115, identified as Mycobacterium massiliense, a member of the newly created taxon of Mycobacterium abscessus subspecies bolletii comb. nov.

Matched MeSH terms: Genome, Bacterial*
Genome-wide prediction and annotation of Burkholderia pseudomallei AraC/XylS family transcription regulator

Lim BS, Chong CE, Zamrod Z, Nathan S, Mohamed R

In Silico Biol. (Gedrukt), 2007;7(4-5):389-97.
PMID: 18391231

Many members of the AraC/XylS family transcription regulator have been proven to play a critical role in regulating bacterial virulence factors in response to environmental stress. By using the Hidden Markov Model (HMM) profile built from the alignment of a 99 amino acid conserved domain sequence of 273 AraC/XylS family transcription regulators, we detected a total of 45 AraC/XylS family transcription regulators in the genome of the Gram-negative pathogen, Burkholderia pseudomallei. Further in silico analysis of each detected AraC/XylS family transcription regulatory protein and its neighboring genes allowed us to make a first-order guess on the role of some of these transcription regulators in regulating important virulence factors such as those involved in three type III secretion systems and biosynthesis of pyochelin, exopolysaccharide (EPS) and phospholipase C. This paper has demonstrated an efficient and systematic genome-wide scale prediction of the AraC/XylS family that can be applied to other protein families.

Matched MeSH terms: Genome, Bacterial*
Fulltext Genome-wide mosaicism within Mycobacterium abscessus: evolutionary and epidemiological implications

Sapriel G, Konjek J, Orgeur M, Bouri L, Frézal L, Roux AL, et al.

BMC Genomics, 2016 Feb 17;17:118.
PMID: 26884275 DOI: 10.1186/s12864-016-2448-1

In mycobacteria, conjugation differs from the canonical Hfr model, but is still poorly understood. Here, we quantified this evolutionary processe in a natural mycobacterial population, taking advantage of a large clinical strain collection of the emerging pathogen Mycobacterium abscessus (MAB).

Matched MeSH terms: Genome, Bacterial*
Fulltext Genome-wide mapping of the RNA targets of the Pseudomonas aeruginosa riboregulatory protein RsmN

Romero M, Silistre H, Lovelock L, Wright VJ, Chan KG, Hong KW, et al.

Nucleic Acids Res, 2018 Jul 27;46(13):6823-6840.
PMID: 29718466 DOI: 10.1093/nar/gky324

Pseudomonads typically carry multiple non-identical alleles of the post-transcriptional regulator rsmA. In Pseudomonas aeruginosa, RsmN is notable in that its structural rearrangement confers distinct and overlapping functions with RsmA. However, little is known about the specificities of RsmN for its target RNAs and overall impact on the biology of this pathogen. We purified and mapped 503 transcripts directly bound by RsmN in P. aeruginosa. About 200 of the mRNAs identified encode proteins of demonstrated function including some determining acute and chronic virulence traits. For example, RsmN reduces biofilm development both directly and indirectly via multiple pathways, involving control of Pel exopolysaccharide biosynthesis and c-di-GMP levels. The RsmN targets identified are also shared with RsmA, although deletion of rsmN generally results in less pronounced phenotypes than those observed for ΔrsmA or ΔrsmArsmNind mutants, probably as a consequence of different binding affinities. Targets newly identified for the Rsm system include the small non-coding RNA CrcZ involved in carbon catabolite repression, for which differential binding of RsmN and RsmA to specific CrcZ regions is demonstrated. The results presented here provide new insights into the intricacy of riboregulatory networks involving multiple but distinct RsmA homologues.

Matched MeSH terms: Genome, Bacterial
Genome-scale metabolic models as platforms for strain design and biological discovery

Mienda BS

J Biomol Struct Dyn, 2017 Jul;35(9):1863-1873.
PMID: 27251747 DOI: 10.1080/07391102.2016.1197153

Genome-scale metabolic models (GEMs) have been developed and used in guiding systems' metabolic engineering strategies for strain design and development. This strategy has been used in fermentative production of bio-based industrial chemicals and fuels from alternative carbon sources. However, computer-aided hypotheses building using established algorithms and software platforms for biological discovery can be integrated into the pipeline for strain design strategy to create superior strains of microorganisms for targeted biosynthetic goals. Here, I described an integrated workflow strategy using GEMs for strain design and biological discovery. Specific case studies of strain design and biological discovery using Escherichia coli genome-scale model are presented and discussed. The integrated workflow presented herein, when applied carefully would help guide future design strategies for high-performance microbial strains that have existing and forthcoming genome-scale metabolic models.

Matched MeSH terms: Genome, Bacterial/genetics*
Genome-scale metabolic models as platforms for identification of novel genes as antimicrobial drug targets

Mienda BS, Salihu R, Adamu A, Idris S

Future Microbiol, 2018 03;13:455-467.
PMID: 29469596 DOI: 10.2217/fmb-2017-0195

The growing number of multidrug-resistant pathogenic bacteria is becoming a world leading challenge for the scientific community and for public health. However, advances in high-throughput technologies and whole-genome sequencing of bacterial pathogens make the construction of bacterial genome-scale metabolic models (GEMs) increasingly realistic. The use of GEMs as an alternative platforms will expedite identification of novel unconditionally essential genes and enzymes of target organisms with existing and forthcoming GEMs. This approach will follow the existing protocol for construction of high-quality GEMs, which could ultimately reduce the time, cost and labor-intensive processes involved in identification of novel antimicrobial drug targets in drug discovery pipelines. We discuss the current impact of existing GEMs of selected multidrug-resistant pathogenic bacteria for identification of novel antimicrobial drug targets and the challenges of closing the gap between genome-scale metabolic modeling and conventional experimental trial-and-error approaches in drug discovery pipelines.

Matched MeSH terms: Genome, Bacterial/genetics*
Fulltext Genome-Wide Transcription Study of Cryptococcus neoformans H99 Clinical Strain versus Environmental Strains

Movahed E, Munusamy K, Tan GM, Looi CY, Tay ST, Wong WF

PLoS One, 2015;10(9):e0137457.
PMID: 26360021 DOI: 10.1371/journal.pone.0137457

The infection of Cryptococcus neoformans is acquired through the inhalation of desiccated yeast cells and basidiospores originated from the environment, particularly from bird's droppings and decaying wood. Three environmental strains of C. neoformans originated from bird droppings (H4, S48B and S68B) and C. neoformans reference clinical strain (H99) were used for intranasal infection in C57BL/6 mice. We showed that the H99 strain demonstrated higher virulence compared to H4, S48B and S68B strains. To examine if gene expression contributed to the different degree of virulence among these strains, a genome-wide microarray study was performed to inspect the transcriptomic profiles of all four strains. Our results revealed that out of 7,419 genes (22,257 probes) examined, 65 genes were significantly up-or down-regulated in H99 versus H4, S48B and S68B strains. The up-regulated genes in H99 strain include Hydroxymethylglutaryl-CoA synthase (MVA1), Mitochondrial matrix factor 1 (MMF1), Bud-site-selection protein 8 (BUD8), High affinity glucose transporter 3 (SNF3) and Rho GTPase-activating protein 2 (RGA2). Pathway annotation using DAVID bioinformatics resource showed that metal ion binding and sugar transmembrane transporter activity pathways were highly expressed in the H99 strain. We suggest that the genes and pathways identified may possibly play crucial roles in the fungal pathogenesis.

Matched MeSH terms: Genome, Bacterial*
Fulltext Genome-Wide Discovery of Genes Required for Capsule Production by Uropathogenic Escherichia coli

Goh KGK, Phan MD, Forde BM, Chong TM, Yin WF, Chan KG, et al.

mBio, 2017 10 24;8(5).
PMID: 29066548 DOI: 10.1128/mBio.01558-17

Uropathogenic Escherichia coli (UPEC) is a major cause of urinary tract and bloodstream infections and possesses an array of virulence factors for colonization, survival, and persistence. One such factor is the polysaccharide K capsule. Among the different K capsule types, the K1 serotype is strongly associated with UPEC infection. In this study, we completely sequenced the K1 UPEC urosepsis strain PA45B and employed a novel combination of a lytic K1 capsule-specific phage, saturated Tn5 transposon mutagenesis, and high-throughput transposon-directed insertion site sequencing (TraDIS) to identify the complement of genes required for capsule production. Our analysis identified known genes involved in capsule biosynthesis, as well as two additional regulatory genes (mprA and lrhA) that we characterized at the molecular level. Mutation of mprA resulted in protection against K1 phage-mediated killing, a phenotype restored by complementation. We also identified a significantly increased unidirectional Tn5 insertion frequency upstream of the lrhA gene and showed that strong expression of LrhA induced by a constitutive Pcl promoter led to loss of capsule production. Further analysis revealed loss of MprA or overexpression of LrhA affected the transcription of capsule biosynthesis genes in PA45B and increased sensitivity to killing in whole blood. Similar phenotypes were also observed in UPEC strains UTI89 (K1) and CFT073 (K2), demonstrating that the effects were neither strain nor capsule type specific. Overall, this study defined the genome of a UPEC urosepsis isolate and identified and characterized two new regulatory factors that affect UPEC capsule production.IMPORTANCE Urinary tract infections (UTIs) are among the most common bacterial infections in humans and are primarily caused by uropathogenic Escherichia coli (UPEC). Many UPEC strains express a polysaccharide K capsule that provides protection against host innate immune factors and contributes to survival and persistence during infection. The K1 serotype is one example of a polysaccharide capsule type and is strongly associated with UPEC strains that cause UTIs, bloodstream infections, and meningitis. The number of UTIs caused by antibiotic-resistant UPEC is steadily increasing, highlighting the need to better understand factors (e.g., the capsule) that contribute to UPEC pathogenesis. This study describes the original and novel application of lytic capsule-specific phage killing, saturated Tn5 transposon mutagenesis, and high-throughput transposon-directed insertion site sequencing to define the entire complement of genes required for capsule production in UPEC. Our comprehensive approach uncovered new genes involved in the regulation of this key virulence determinant.

Matched MeSH terms: Genome, Bacterial*
Genome size variation among recent human isolates of Salmonella typhi

Thong KL, Puthucheary SD, Pang T

Res. Microbiol., 1997 Mar-Apr;148(3):229-35.
PMID: 9765803

We performed genome size estimation of 17 recent human isolates of Salmonella typhi from geographically diverse regions using pulsed-field gel electrophoresis (PFGE) after digestion of chromosomal DNA with restriction endonucleases XbaI (5'-TCTAGA-3'), AvrII (5'-CCTAGG-3') and SpeI (5'-ACTAGT-3'), and summation of the sizes of restriction fragments obtained. All 17 isolates had circular chromosomes, and genome sizes differed by as much as 959 kb, ranging from 3,964 to 4,923 kb (mean genome size = 4,528 kb). The data obtained confirm the usefulness of PFGE in studies of bacterial genome size and are in agreement with recent results indicating considerable genetic diversity and genomic plasticity of S. typhi. The variation in genome sizes noted may be relevant to the observed biological properties of this important human pathogen, including its virulence.

Matched MeSH terms: Genome, Bacterial*

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