1
|
O'Grady HM, Harrison R, Snedeker K, Trufen L, Yue P, Ward L, Fifen A, Jamieson P, Weiss A, Coulthard J, Lynch T, Croxen MA, Li V, Pabbaraju K, Wong A, Zhou HY, Dingle TC, Hellmer K, Berenger BM, Fonseca K, Lin YC, Evans D, Conly JM. A two-ward acute care hospital outbreak of SARS-CoV-2 delta variant including a point-source outbreak associated with the use of a mobile vital signs cart and sub-optimal doffing of personal protective equipment. J Hosp Infect 2023; 131:1-11. [PMID: 36195200 PMCID: PMC9527227 DOI: 10.1016/j.jhin.2022.09.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/16/2022] [Accepted: 09/27/2022] [Indexed: 01/25/2023]
Abstract
BACKGROUND The arrival of the Delta variant of SARS-CoV-2 was associated with increased transmissibility and illness of greater severity. Reports of nosocomial outbreaks of Delta variant COVID-19 in acute care hospitals have been described but control measures varied widely. AIM Epidemiological investigation of a linked two-ward COVID-19 Delta variant outbreak was conducted to elucidate its source, risk factors, and control measures. METHODS Investigations included epidemiologic analysis, detailed case review serial SARS-CoV-2 reverse transcriptase-polymerase chain reaction (RT-PCR) testing of patients and healthcare workers (HCWs), viral culture, environmental swabbing, HCW-unaware personal protective equipment (PPE) audits, ventilation assessments, and the use of whole genome sequencing (WGS). FINDINGS This linked two-ward outbreak resulted in 17 patient and 12 HCW cases, despite an 83% vaccination rate. In this setting, suboptimal adherence and compliance to PPE protocols, suboptimal hand hygiene, multi-bedded rooms, and a contaminated vital signs cart with potential fomite or spread via the hands of HCWs were identified as significant risk factors for nosocomial COVID-19 infection. Sudden onset of symptoms, within 72 h, was observed in 79% of all Ward 2 patients, and 93% of all cases (patients and HCWs) on Ward 2 occurred within one incubation period, consistent with a point-source outbreak. RT-PCR assays showed low cycle threshold (CT) values, indicating high viral load from environmental swabs including the vital signs cart. WGS results with ≤3 SNP differences between specimens were observed. CONCLUSION Outbreaks on both wards settled rapidly, within 3 weeks, using a `back-to-basics' approach without extraordinary measures or changes to standard PPE requirements. Strict adherence to recommended PPE, hand hygiene, education, co-operation from HCWs, including testing and interviews, and additional measures such as limiting movement of patients and staff temporarily were all deemed to have contributed to prompt resolution of the outbreak.
Collapse
Affiliation(s)
- H M O'Grady
- Infection Prevention and Control, Alberta Health Services, Calgary, Alberta, Canada
| | - R Harrison
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada; Workplace Health and Safety, Alberta Health Services, Edmonton, Alberta, Canada
| | - K Snedeker
- Provincial Population and Public Health, Alberta Health Services, Calgary, Alberta, Canada
| | - L Trufen
- Workplace Health and Safety, Alberta Health Services, Edmonton, Alberta, Canada
| | - P Yue
- Infection Prevention and Control, Alberta Health Services, Calgary, Alberta, Canada
| | - L Ward
- Infection Prevention and Control, Alberta Health Services, Calgary, Alberta, Canada
| | - A Fifen
- Infection Prevention and Control, Alberta Health Services, Calgary, Alberta, Canada
| | - P Jamieson
- Department of Family Medicine, University of Calgary and Alberta Health Services, Calgary, Alberta, Canada; Site Administration, Foothills Medical Centre, Alberta Health Services, Calgary, Alberta, Canada
| | - A Weiss
- Site Administration, Foothills Medical Centre, Alberta Health Services, Calgary, Alberta, Canada
| | - J Coulthard
- Site Administration, Foothills Medical Centre, Alberta Health Services, Calgary, Alberta, Canada
| | - T Lynch
- Department of Pathology & Laboratory Medicine, University of Calgary and Alberta Health Services, Calgary, Alberta, Canada; Genomics and Bioinformatics, Alberta Public Health Laboratory, Alberta Precision Laboratories, Calgary, Alberta, Canada; Alberta Public Health Laboratory, Alberta Precision Laboratories, Calgary, Alberta, Canada
| | - M A Croxen
- Alberta Public Heath Laboratory, Alberta Precision Laboratories, Edmonton, Alberta, Canada; Department of Laboratory Medicine, University of Alberta, Edmonton, Alberta, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada
| | - V Li
- Alberta Public Heath Laboratory, Alberta Precision Laboratories, Edmonton, Alberta, Canada
| | - K Pabbaraju
- Alberta Public Health Laboratory, Alberta Precision Laboratories, Calgary, Alberta, Canada
| | - A Wong
- Alberta Public Health Laboratory, Alberta Precision Laboratories, Calgary, Alberta, Canada
| | - H Y Zhou
- Alberta Public Health Laboratory, Alberta Precision Laboratories, Calgary, Alberta, Canada; Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - T C Dingle
- Department of Pathology & Laboratory Medicine, University of Calgary and Alberta Health Services, Calgary, Alberta, Canada; Alberta Public Health Laboratory, Alberta Precision Laboratories, Calgary, Alberta, Canada
| | - K Hellmer
- Site Administration, Foothills Medical Centre, Alberta Health Services, Calgary, Alberta, Canada
| | - B M Berenger
- Department of Pathology & Laboratory Medicine, University of Calgary and Alberta Health Services, Calgary, Alberta, Canada; Alberta Public Health Laboratory, Alberta Precision Laboratories, Calgary, Alberta, Canada
| | - K Fonseca
- Alberta Public Health Laboratory, Alberta Precision Laboratories, Calgary, Alberta, Canada; Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Y-C Lin
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada; Department of Medical Microbiology & Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - D Evans
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada; Department of Medical Microbiology & Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - J M Conly
- Infection Prevention and Control, Alberta Health Services, Calgary, Alberta, Canada; Department of Pathology & Laboratory Medicine, University of Calgary and Alberta Health Services, Calgary, Alberta, Canada; Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada; Department of Medicine, University of Calgary and Alberta Health Services, Calgary, Alberta, Canada; W21C Research and Innovation Centre, O'Brien Institute for Public Health, University of Calgary, Calgary, Alberta, Canada; Snyder Institute for Chronic Diseases, University of Calgary and Alberta Health Services, Calgary, Alberta, Canada.
| |
Collapse
|
2
|
Pabbaraju K, Fonseca K, Wong S, Koch MW, Joseph JT, Tipples GA, Tellier R. Genetic characterization of measles virus genotype D6 subacute sclerosing panencephalitis case, Alberta, Canada. J Neurovirol 2018; 24:720-729. [PMID: 30291564 DOI: 10.1007/s13365-018-0668-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 07/09/2018] [Accepted: 07/26/2018] [Indexed: 11/29/2022]
Abstract
Subacute sclerosing panencephalitis (SSPE) is a progressive and eventually fatal neurological disease arising from a persistent infection with measles virus (MV) acquired at a young age. SSPE measles virus strains are defective and unable to produce progeny virions, due to multiple and extensive mutations in a number of key genes. We sequenced the full MV genome from our recently reported SSPE case, which typed as genotype D6, and compared it with other genotype D6 wild type and SSPE sequences. The Alberta D6 strain was significantly different from other reported SSPE D6 sequences. Mutations were observed in all the genes of the Alberta strain, with the greatest sequence divergence noted in the M gene with 17.6% nucleotide and 31% amino acid variation. The L gene showed the least variation with 1.3% nucleotide and 0.7% amino acid differences respectively. The nucleotide variability for 15,672 bases of the complete genome compared to the wild type and other SSPE D6 strains was around 3%.
Collapse
Affiliation(s)
- K Pabbaraju
- Provincial Laboratory for Public Health, Calgary, Alberta, Canada.
| | - K Fonseca
- Provincial Laboratory for Public Health, Calgary, Alberta, Canada.,Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - S Wong
- Provincial Laboratory for Public Health, Calgary, Alberta, Canada
| | - M W Koch
- Departments of Clinical Neurosciences and Community Health Sciences, University of Calgary, Calgary, Alberta, Canada
| | - J T Joseph
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
| | - G A Tipples
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada.,Provincial Laboratory for Public Health, Edmonton, Alberta, Canada
| | - R Tellier
- Provincial Laboratory for Public Health, Calgary, Alberta, Canada.,Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
| |
Collapse
|
3
|
Prakash R, Pabbaraju K, Wong S, Wong A, Tellier R, Kaler KVIS. Droplet Microfluidic Chip Based Nucleic Acid Amplification and Real-Time Detection of Influenza Viruses. J Electrochem Soc 2014; 161:B3083-B3093. [PMID: 32287356 PMCID: PMC7105149 DOI: 10.1149/2.013402jes] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 12/13/2013] [Indexed: 06/11/2023]
Abstract
Miniaturized bio-diagnostic devices have the potential to allow for rapid pathogen screening in clinical patient samples, as a low cost and portable alternative to conventional bench-top equipment. Miniaturization of key bio-diagnostic techniques, such as: nucleic acid detection and quantification, polymerase chain reaction (PCR), DNA fingerprinting, enzyme linked immunosorbent assay (ELISA), results in substantial reduction of reaction volumes (expensive samples/reagents) and shorter reaction times. Droplet microfluidics (DMF) is one of several miniaturized bio-sample handling techniques available for manipulating clinical samples and reagents in microliter (10-6 L) to picoliter (10-12 L) volume regime. Electro-actuation of sample and reagent in the form of droplets in the aforementioned volume regime, using dielectrophoresis (DEP) and/or Electrowetting (EW) are achieved by means of patterned, insulated metal electrodes on one or more substrates. In this work, we have utilized electro-actuation based DMF technology, integrated with suitably tailored resistive micro-heaters and temperature sensors, to achieve chip based real-time, quantitative PCR (qRT-PCR). This qRT-PCR micro-device was utilized to detect and quantify the presence of influenza A and C virus nucleic acids, using in-vitro synthesized viral RNA segments. The experimental analysis of the DMF micro-device confirms its capabilities in qRT-PCR based detection and quantification of pathogen samples, with accuracy levels comparable to established commercial bench-top equipment (PCR efficiency ∼95%). The limit of detection (LOD) of the chip based qRT-PCR technique was estimated to be ∼5 copies of template RNA per PCR reaction.
Collapse
Affiliation(s)
- R Prakash
- Biosystems Research and Applications Group, Schulich School of Engineering, University of Calgary, Calgary, Alberta AB T2N 1N4, Canada
| | - K Pabbaraju
- Provincial Laboratory for Public Health of Alberta, ProvLAB, Calgary AB T2N4W4, Canada
| | - S Wong
- Provincial Laboratory for Public Health of Alberta, ProvLAB, Calgary AB T2N4W4, Canada
| | - A Wong
- Provincial Laboratory for Public Health of Alberta, ProvLAB, Calgary AB T2N4W4, Canada
| | - R Tellier
- Provincial Laboratory for Public Health of Alberta, ProvLAB, Calgary AB T2N4W4, Canada
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - K V I S Kaler
- Biosystems Research and Applications Group, Schulich School of Engineering, University of Calgary, Calgary, Alberta AB T2N 1N4, Canada
| |
Collapse
|
4
|
Pabbaraju K, Wong S, Song J, Singh AE, Drews S, Read RR. P2.030 Utility of Neisseria GonorrhoeaPositive APTIMA Specimens to Assess Strain Diversity and Antibiotic Resistance. Br J Vener Dis 2013. [DOI: 10.1136/sextrans-2013-051184.0295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
|
5
|
Drews SJ, Pabbaraju K, Wong S, Tokaryk KL, May-Hadford J, Lee B, Tellier R, Louie M. Surveillance of autopsy cases for D222G substitutions in haemagglutinin of the pandemic (H1N1) 2009 virus in Alberta, Canada. Clin Microbiol Infect 2010; 17:582-4. [PMID: 20718801 DOI: 10.1111/j.1469-0691.2010.03341.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Pandemic (H1N1) 2009 virus-positive specimens were collected from autopsy patients and matched to pandemic (H1N1) 2009 virus-positive nasopharyngeal specimens from community control patients and pandemic (H1N1) 2009 virus-positive specimens from intensive-care unit (ICU) patients. Specimens were analysed for polymorphisms at amino acid 222 of the haemagglutinin (HA) glycoprotein. Whereas some specimens from autopsy patients were positive for D222N, none was positive for D222G. All control patient specimens were wild-type D222. D222G polymorphisms were also identified in a subset of ICU patients with admixtures of D222G and D222 and of D222N, D222G and D222 present. The relevance of D222N and D222G to influenza pathogenesis and transmissibility currently remains unclear.
Collapse
Affiliation(s)
- S J Drews
- Provincial Laboratory for Public Health Microbiology, Calgary Site, Calgary, AB, Canada.
| | | | | | | | | | | | | | | |
Collapse
|
6
|
Pabbaraju K, Wong S, Wong A, Shokoples S, Fonseca K, Pang X. PIV-10 Development and validation of a real time RT-PCR assay for the typing of swine origin influenza H1N1 virus (S-OIV). J Clin Virol 2009. [DOI: 10.1016/s1386-6532(09)70106-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
7
|
Halyk L, Wong S, Lee B, Pabbaraju K, Fox J. O16 Etiological diagnosis of respiratory outbreaks using a combination of antigen and nucleic acid amplification tests. Int J Antimicrob Agents 2009. [PMCID: PMC7172065 DOI: 10.1016/s0924-8579(09)70163-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
8
|
Khurana V, Wong S, Deserres J, Pabbaraju K, Fox J. P213 Identification of adenovirus serotypes by sequencing directly from clinical samples. Int J Antimicrob Agents 2009. [DOI: 10.1016/s0924-8579(09)70432-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
9
|
Wong S, Pabbaraju K, Zarra D, Tokaryk K, Fox J. P199 Evaluation of a multiplex real-time assay for quantification of human adenoviruses in different specimen types. Int J Antimicrob Agents 2009. [DOI: 10.1016/s0924-8579(09)70418-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
10
|
Smieja M, Singh P, Moss L, Pabbaraju K, Wong S, Fox J, Loeb M. P262 Self or parent-collected nasal mid-turbinate flocked swabs versus nasopharyngeal swabs for influenza diagnosis in a community-based study. Int J Antimicrob Agents 2009. [DOI: 10.1016/s0924-8579(09)70481-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
11
|
Zahariadis G, Balutis K, Wong A, Wong S, Pabbaraju K, Severini A, Tilley P, Fox J. P215 Evaluation of extraction and genotyping methods for human papillomavirus detection and analysis from liquid-based cytology specimens. Int J Antimicrob Agents 2009. [DOI: 10.1016/s0924-8579(09)70434-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
12
|
Wong S, Pabbaraju K, Khurana V, Pang X, Fox J. Nucleic acid amplification assays for investigation of respiratory viruses. J Clin Virol 2006. [PMCID: PMC7128877 DOI: 10.1016/s1386-6532(06)80763-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
13
|
Wong S, Pabbaraju K, Ho K, Khurana V, Fox J. Influenza A detection, typing and assessment of antiviral resistance. J Clin Virol 2006. [PMCID: PMC7128773 DOI: 10.1016/s1386-6532(06)80762-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
14
|
Kalir S, McClure J, Pabbaraju K, Southward C, Ronen M, Leibler S, Surette MG, Alon U. Ordering genes in a flagella pathway by analysis of expression kinetics from living bacteria. Science 2001; 292:2080-3. [PMID: 11408658 DOI: 10.1126/science.1058758] [Citation(s) in RCA: 264] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The recent advances in large-scale monitoring of gene expression raise the challenge of mapping systems on the basis of kinetic expression data in living cells. To address this, we measured promoter activity in the flagellar system of Escherichia coli at high accuracy and temporal resolution by means of reporter plasmids. The genes in the pathway were ordered by analysis algorithms without dependence on mutant strains. The observed temporal program of transcription was much more detailed than was previously thought and was associated with multiple steps of flagella assembly.
Collapse
Affiliation(s)
- S Kalir
- Department of Molecular Cell Biology, Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | | | | | | | | | | | | |
Collapse
|
15
|
Abstract
Intervening sequences (IVSs) occur sporadically in the rrl (ribosomal RNA large) genes for 23S ribosomal RNA (rRNA) at helix-25 (base pair 550) and helix 45 (base pair 1170) in several bacterial genera, including Salmonella, Yersinia, Proteus, and Providencia, representing the Enterobacteriaceae, but are missing from other genera such as Escherichia. These sequences are transcribed, but later excised without re-ligation during RNaseIII processing of the rRNA, resulting in fragmented 23S rRNA. The IVSs from 22 strains of the SARB (Salmonella Reference Collection B) set were amplified by PCR and sequenced.IVSs with 90% or more sequence identity were placed in the same family; Salmonella has three families of IVSs in helix-25 (A, B, and C) and two in helix-45 (M and O). The rRNA secondary structure for the IVSs predicted from the mfold program reveals a primary stem of about 14bp, which is the postulated RNaseIII cleavage site, and a secondary region of stems and loops. The primary stem is considerably well conserved, with a high rate of compensatory mutations (positional covariants), confirming the reality of the secondary structure and indicating that removal of the IVSs exerts a positive selective pressure to retain the secondary structure. The pattern of possession and presence of families of IVSs was diverse and could not be related to the proposed ancestry of the strains as revealed by the multi-locus enzyme electrophoresis pattern of the strains, suggesting that the IVSs are transferred between strains by lateral transfer. Helix-25 IVSs from families A, B, and C of Salmonella and D of Proteus, which share almost identical primary stems, are placed in superfamily I, while the primary stems of other IVSs from Proteus and Providencia are unrelated to superfamily I and are thus placed into superfamily II; this indicates lateral transfer of members of superfamily I between Proteus and Salmonella, but an independent origin of IVSs of superfamily II in Proteus and Providencia.
Collapse
Affiliation(s)
- K Pabbaraju
- Salmonella Genetic Stock Centre, Department of Biological Sciences, University of Calgary, Alberta, T2N 1N4, Calgary, Canada
| | | |
Collapse
|
16
|
Pabbaraju K, Miller WL, Sanderson KE. Distribution of intervening sequences in the genes for 23S rRNA and rRNA fragmentation among strains of the Salmonella reference collection B (SARB) and SARC sets. J Bacteriol 2000; 182:1923-9. [PMID: 10714998 PMCID: PMC101879 DOI: 10.1128/jb.182.7.1923-1929.2000] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Intervening sequences (IVSs) occur sporadically in several bacterial genera in the genes for 23S rRNA at relatively conserved locations. They are cleaved after transcription and lead to the presence of fragmented rRNA, which is incorporated into the ribosomes without religation but is nevertheless functional. The fragmentation of rRNA and the number of IVSs in all 72 strains of the Salmonella Reference Collection B set and 16 strains of the Salmonella Reference Collection C set, which have been established on the basis of multilocus enzyme electrophoresis (MLEE), were analyzed in the present study. Fragmentation of 23S rRNA was restricted to conserved cleavage sites located at bp 550 (helix 25) and bp 1170 (helix 45), locations where IVSs have been reported. Random cleavage at sites where IVSs could not be detected was not seen. Uncleaved IVSs were not detected in any case; thus, the IVSs invariably led to rRNA fragmentation, indicating a strong selection for maintenance of RNase III cleavage sites. The distribution of the number of IVSs carried by the different strains in the seven rrl genes is diverse, and the pattern of IVS possession could not be related to the MLEE pattern among the various Salmonella strains tested; this indicates that the IVSs are frequently exchanged between strains by lateral transfer. All eight subspecies of the genus Salmonella, including subspecies V represented by Salmonella bongori, have IVSs in both helix 25 and helix 45; this indicates that IVSs entered the genus after its divergence from Escherichia coli (more than 100 million years ago) but before separation of the genus Salmonella into many forms or that they were in the ancestor but have been lost from Escherichia.
Collapse
MESH Headings
- Base Pairing/genetics
- Biological Specimen Banks
- Conserved Sequence/genetics
- Endoribonucleases/metabolism
- Escherichia coli/genetics
- Escherichia coli Proteins
- Genes, Bacterial/genetics
- Genetic Variation/genetics
- Models, Genetic
- Molecular Weight
- Phylogeny
- Polymerase Chain Reaction
- RNA Processing, Post-Transcriptional/genetics
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 23S/metabolism
- Recombination, Genetic/genetics
- Regulatory Sequences, Nucleic Acid/genetics
- Regulatory Sequences, Nucleic Acid/physiology
- Ribonuclease III
- Salmonella/classification
- Salmonella/genetics
- rRNA Operon/genetics
Collapse
Affiliation(s)
- K Pabbaraju
- Salmonella Genetic Stock Centre, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4.
| | | | | |
Collapse
|
17
|
Miller WL, Pabbaraju K, Sanderson KE. Fragmentation of 23S rRNA in strains of Proteus and Providencia results from intervening sequences in the rrn (rRNA) genes. J Bacteriol 2000; 182:1109-17. [PMID: 10648538 PMCID: PMC94388 DOI: 10.1128/jb.182.4.1109-1117.2000] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Intervening sequences (IVSs) were originally identified in the rrl genes for 23S rRNA (rrl genes, for large ribosomal subunit, part of rrn operon encoding rRNA) of Salmonella enterica serovars Typhimurium LT2 and Arizonae. These sequences are transcribed but later removed during RNase III processing of the rRNA, resulting in fragmentation of the 23S species; IVSs are uncommon, but have been reported in at least 10 bacterial genera. Through PCR amplification of IVS-containing regions of the rrl genes we showed that most Proteus and Providencia strains contain IVSs similar to those of serovar Typhimurium in distribution and location in rrl genes. By extraction and Northern blotting of rRNA, we also found that these IVSs result in rRNA fragmentation. We report the first finding of two very different sizes of IVS (113 bp and 183 to 187 bp) in different rrl genes in the same strain, in helix 25 of Proteus and Providencia spp.; IVSs from helix 45 are 113 to 123 bp in size. Analysis of IVS sequence and postulated secondary structure reveals striking similarities of Proteus and Providencia IVSs to those of serovar Typhimurium, with the stems of the smaller IVSs from helix 25 being similar to those of Salmonella helix 25 IVSs and with both the stem and the central loop domain of helix 45 IVSs being similar. Thus, IVSs of related sequences are widely distributed throughout the Enterobacteriaceae, in Salmonella, Yersinia, Proteus, and Providencia spp., but we did not find them in Escherichia coli, Citrobacter, Enterobacter, Klebsiella, or Morganella spp.; the sporadic distribution of IVSs of related sequence indicates that lateral genetic transfer has occurred.
Collapse
Affiliation(s)
- W L Miller
- Salmonella Genetic Stock Centre, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4
| | | | | |
Collapse
|