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Novel plasmids in multidrug-resistant Shigella flexneri serotypes from Pakistan

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Abstract

Shigellosis is the main cause of food and waterborne diarrhea and is an emerging threat to human health. The current study characterized the indigenous multidrug-resistant Shigella flexneri serotypes for their plasmid profiles and genetic diversity, to characterize the plasmid evolutionary patterns and distribution. In total, 199 identified S. flexneri isolates belonging to six different serotypes were analyzed for plasmid profiling, followed by an analysis of whole genome sequencing. All isolates of S. flexneri resistant to antibiotics harbored multiple copies of plasmids with sizes ranging from 1.25 kbp to 9.4 kbp. These isolates were clustered into 22 distinct plasmid patterns, labeled as p1–p22. Among these, p1 (24%) and p10 (13%) were the predominant plasmid profiles. All S. flexneri strains were grouped into 12 clades with a 75% similarity level. Also, a significant association was observed among the plasmid patterns, p23 and p17 with the drug-resistant patterns AMC, SXT, C (19.5%) and OFX, AMC, NA, CIP (13.5%), respectively. Moreover, the most widespread plasmid patterns p4, p10, and p1 showed a significant association with the serotypes 1b (29.16%), 2b (36%), and 7a (100%), respectively. After plasmid sequence assembly and annotation analysis, a variety of small plasmids that vary in size from 973 to 6200 bp were discovered. Many of these plasmids displayed high homology and coverage with plasmids from non-S. flexneri. Several novel plasmids of small size were discovered in multidrug-resistant S. flexneri. The data also showed that plasmid profile analysis is more consistent than antibiotic susceptibility pattern analysis for identifying epidemic strains of S. flexneri isolated in Pakistan.

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References

  • Agtini MD, Soeharno R, Lesmana M et al (2005) The burden of diarrhoea, shigellosis, and cholera in North Jakarta, Indonesia: findings from 24 months surveillance. BMC Infect Dis 5:89

    Article  PubMed  PubMed Central  Google Scholar 

  • Ahmed B, Shakoori FR, Ali SS et al (2009) antimicrobial resistance and plasmid profile analysis of clinically isolated Shigella dysenteriae in Azad Kashmir, Pakistan. Pak J Zool 41(6):495–503

    CAS  Google Scholar 

  • Aziz KMA, Wells JG, Boyce JM et al (1982) Patterns of Shigella infection in families in Rural Bangladesh. Am J Trop Med Hyg 31:1015–1020

    Article  PubMed  Google Scholar 

  • Banner DW, Kokkinidis M, Tsernoglou D (1987) Structure of the ColE1 rop protein at 1.7A resolution. J Mol Biol 196:657–675

    Article  CAS  PubMed  Google Scholar 

  • Boyd AC, Archer JA, Sherratt DJ (1989) Characterization of the ColE1 mobilization region and its protein products. Mol Gen Genet 217:488–498

    Article  CAS  PubMed  Google Scholar 

  • Burian J, Ausió J, Phipps B et al (2003) Hexamerization of RepA from the Escherichia coli plasmid pKL1. Biochemistry 42:10282–10287

    Article  CAS  PubMed  Google Scholar 

  • Craun GF, Calderon RL, Craun MF (2005) Outbreaks associated with recreational water in the United States. Int J Environ Health Res 15:243–262

    Article  PubMed  Google Scholar 

  • Davies J, Wright GD (1997) Bacterial resistance to aminoglycoside antibiotics. Trends Microbiol 5:234–240

    Article  CAS  PubMed  Google Scholar 

  • Deatherage DE, Barrick JE (2014) Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq. Methods Mol Biol 1151:165–188

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dutta S, Rajendran K, Roy S et al (2002) Shifting serotypes, plasmid profile analysis and antimicrobial resistance pattern of shigellae strains isolated from Kolkata, India during 1995–2000. Epidemiol Infect 129:235–243

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Farshad S, Sheikhi R, Japoni A et al (2006) Characterization of Shigella Strains in Iran by plasmid profile analysis and PCR amplification of ipa Genes. J Clin Microbiol 44:2879–2883

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kamada K, Hanaoka F, Burley SK (2003) Crystal structure of the MazE/MazF complex: molecular bases of antidote-toxin recognition. Mol Cell 11:875–884

    Article  CAS  PubMed  Google Scholar 

  • Kim C, Mobashery S (2005) Phosphoryl transfer by aminoglycoside 3′-phosphotransferases and manifestation of antibiotic resistance. Bioorg Chem 33:149–158

    Article  PubMed  Google Scholar 

  • Kotloff KL, Winickoff JP, Ivanoff B et al (1999) Global burden of Shigella infections: implications for vaccine development and implementation of control strategies. Bull World Health Organ 77:651–666

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lane BR, Ast JC, Hossler PA et al (1997) Dihydropteroate synthase polymorphisms in Pneumocystis carinii. J Infect Dis 175:482–485

    Article  CAS  PubMed  Google Scholar 

  • Murray GL, Attridge SR, Morona R (2005) Inducible serum resistance in Salmonella typhimurium is dependent on wzzfepE-regulated very long O antigen chains. Microbes Infect 7:1296–1304

    Article  CAS  PubMed  Google Scholar 

  • Nandy S, Mitra U, Rajendran K, Dutta P, Dutta S (2010) Subtype prevalence, plasmid profiles and growing fluoroquinolone resistance in Shigella from Kolkata India (2001–2007): a hospital-based study. Trop Med Int Heal 15:1499–1507

    Article  CAS  Google Scholar 

  • Nisa I, Qasim M, Driessen A et al (2020) Molecular epidemiology of Shigella flexneri isolated from pediatrics in a diarrhea-endemic area of Khyber Pakhtunkhwa, Pakistan. Eur J Clin Microbiol Infect Dis. https://doi.org/10.1007/s10096-020-03811-0

    Article  PubMed  Google Scholar 

  • Nisa I, Qasim M, Yasin N et al (2020b) Shigella flexneri: an emerging pathogen. Folia Microbiol (praha). https://doi.org/10.1007/s12223-020-00773-w

    Article  PubMed  Google Scholar 

  • Nisa I, Qasim M, Driessen A et al (2021) Prevalence and associated risk factors of Shigella flexneri isolated from drinking water and retail raw foods in Peshawar. Pakistan J Food Sci 86:2579–2589

    Article  CAS  PubMed  Google Scholar 

  • Nisa I, Haroon M, Driessen A et al (2022) Antimicrobial resistance of Shigella flexneri in Pakistani pediatric population reveals an increased trend of third-generation cephalosporin resistance. Curr Microbiol 79:1–10

    Article  Google Scholar 

  • Nurizzo D, Shewry SC, Perlin MH et al (2003) The crystal structure of aminoglycoside-3’-phosphotransferase-IIa, an enzyme responsible for antibiotic resistance. J Mol Biol 327:491–506

    Article  CAS  PubMed  Google Scholar 

  • Ozenberger BA, Nahlik MS, McIntosh MA (1987) Genetic organization of multiple fep genes encoding ferric enterobactin transport functions in Escherichia coli. J Bacteriol 169:3638–3646

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sakhaei A, Savari M, Shokoohizadeh L et al (2015) Characterization of Shigella strains by plasmid profile analysis and antibiotic susceptibility patterns in a pediatric hospital in Ahvaz. Int J Enteric Pathog 3:29924

    Article  Google Scholar 

  • Sharma A, Kumar S, Divya S (2009) Phenotypic and genotypic characterization of Shigella spp. with reference to its virulence genes and antibiogram analysis from river Narmada. Indian J Microbiol 49:259–265

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Szakál DD, Schneider G, Pál T (2003) A colony blot immune assay to identify enteroinvasive Escherichia coli and Shigella in stool samples. Diagn Microbiol Infect Dis 45:165–171

    Article  Google Scholar 

  • Tacket CO, Shahid N, Huq MI, Alim ARMA, Cohen ML (1984) Usefulness of plasmid profiles for differentiation of Shigella isolates in Bangladesh enteric diseases branch, centers for disease control. J Clin Microbiol 20:300–301

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Talukder KA, Islam Z, Islam MA et al (2003) Phenotypic and genotypic characterization of provisional serotype Shigella flexneri 1c and clonal relationships with 1a and 1b strains isolated in Bangladesh. J Clin Microbiol 41:110–117

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tohyama H, Okami Y, Umezawa H (1987) Nucleotide sequence of the streptomycinphosphotransferase and amidinotransferase genes from Streptomyces griseus. Nucleic Acids Res 15:1819–1833

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Venkatesan MM, Goldberg MB, Rose DJ et al (2001) Complete DNA sequence and analysis of the large virulence plasmid of Shigella flexneri. Infect Immun 69:3271–3285

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wei Y, Murphy ER (2016) Shigella iron acquisition systems and their regulation. Front Cell Infect Microbiol 6:18

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhang S, Meyer R (1997) The relaxosome protein MobC promotes conjugal plasmid mobilization by extending DNA strand separation to the nick site at the origin of transfer. Mol Microbiol 25:509–516

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

The authors would like to acknowledge the staff of the Department of Molecular Microbiology Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherland, Veterinary Research Institute Peshawar, Lady Reading Hospital Peshawar, Pakistan and Kohat University of Science and Technology, Kohat, for their excellent technical assistance. This work was supported by grants from the Higher Education Commission of Pakistan (FTO number 0341-3970-2018). In addition, the current work is a part of Iqbal Nisa’s PhD thesis/dissertation.

Funding

This work was supported by grants from the Higher Education Commission of Pakistan (FTO number 0341-3970-2018).

Author information

Authors and Affiliations

  1. Department of Microbiology, Kohat University of Science and Technology, Kohat, 26000, Pakistan

    Iqbal Nisa & Muhammad Qasim

  2. Department of Microbiology, Women University Swabi, Swabi, Pakistan

    Iqbal Nisa

  3. Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands

    Arnold Driessen & Jeroen Nijland

  4. Department of Microbiology, Abdul Wali Khan University, Mardan, Pakistan

    Hazir Rahman

  5. Mikrobiologisches Institut-Klinische Mikrobiologie, Immunologie Und Hygiene, Universitätsklinikum Erlangen and Friedrich-Alexander Universität (FAU) Erlangen-Nürnberg, 91054, Erlangen, Germany

    Jochen Mattner

Authors
  1. Iqbal Nisa
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  2. Arnold Driessen
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  3. Jeroen Nijland
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  4. Hazir Rahman
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  5. Jochen Mattner
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  6. Muhammad Qasim
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Contributions

All authors contributed to the study conception and design. Material preparation and data collection were performed by IN and analysis was performed by MQ, AD, JN, HR, and JM. The first draft of the manuscript was written by IN and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

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Correspondence to Muhammad Qasim.

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The authors declare that they have no relevant financial or non-financial interests to disclose.

Ethical approval

All procedures followed were in accordance with the ethical standards of the responsible committee on human experimentation (institutional and national) and with the Helsinki Declaration of 1975, as revised in 2000, approved by the Kohat University of Science and Technology, Kohat research and ethical committee.

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Informed consent was obtained from all patients/guardians for being included in the study.

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Communicated by Erko Stackebrandt.

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Nisa, I., Driessen, A., Nijland, J. et al. Novel plasmids in multidrug-resistant Shigella flexneri serotypes from Pakistan. Arch Microbiol 205, 175 (2023). https://doi.org/10.1007/s00203-023-03523-x

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  • DOI: https://doi.org/10.1007/s00203-023-03523-x

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