1
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Cheng YY, Zhou Z, Papadopoulos JM, Zuke JD, Falbel TG, Anantharaman K, Burton BM, Venturelli OS. Efficient plasmid transfer via natural competence in a microbial co-culture. Mol Syst Biol 2023; 19:e11406. [PMID: 36714980 PMCID: PMC9996237 DOI: 10.15252/msb.202211406] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/21/2022] [Accepted: 01/09/2023] [Indexed: 01/31/2023] Open
Abstract
The molecular and ecological factors shaping horizontal gene transfer (HGT) via natural transformation in microbial communities are largely unknown, which is critical for understanding the emergence of antibiotic-resistant pathogens. We investigate key factors shaping HGT in a microbial co-culture by quantifying extracellular DNA release, species growth, and HGT efficiency over time. In the co-culture, plasmid release and HGT efficiency are significantly enhanced than in the respective monocultures. The donor is a key determinant of HGT efficiency as plasmids induce the SOS response, enter a multimerized state, and are released in high concentrations, enabling efficient HGT. However, HGT is reduced in response to high donor lysis rates. HGT is independent of the donor viability state as both live and dead cells transfer the plasmid with high efficiency. In sum, plasmid HGT via natural transformation depends on the interplay of plasmid properties, donor stress responses and lysis rates, and interspecies interactions.
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Affiliation(s)
- Yu-Yu Cheng
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
| | - Zhichao Zhou
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA
| | - James M Papadopoulos
- Department of Chemical & Biological Engineering, University of Wisconsin, Madison, WI, USA
| | - Jason D Zuke
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA
| | - Tanya G Falbel
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA
| | | | - Briana M Burton
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA
| | - Ophelia S Venturelli
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA.,Department of Bacteriology, University of Wisconsin, Madison, WI, USA.,Department of Chemical & Biological Engineering, University of Wisconsin, Madison, WI, USA
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2
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Imanishi I, Iyori K, Také A, Asahina R, Tsunoi M, Hirano R, Uchiyama J, Toyoda Y, Sakaguchi Y, Hayashi S. Antibiotic-resistant status and pathogenic clonal complex of canine Streptococcus canis-associated deep pyoderma. BMC Vet Res 2022; 18:395. [DOI: 10.1186/s12917-022-03482-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 10/22/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Streptococcus canis causes deep pyoderma in canines, which raises concerns about the risk of isolates from lesions acquiring an antibiotic-resistant phenotype. It is necessary to identify effective antibiotics and the characteristics of the pathogenic cluster for S. canis-associated deep pyoderma.
Results
The signalment, molecular typing, and antibiotic-resistant status of S. canis isolated from deep pyoderma lesions (27 strains) and oral cavities (26 strains) were analyzed. Older dogs tended to have S. canis-associated deep pyoderma (15 of 27 dogs over 10 years old). Veterinarians chose quinolones for 10/16 cases (63%), even though the rate of quinolone-resistant strains of S. canis is 38–59%. Although 70% of the strains showed resistance to three or more antibiotic classes (37/53), 94% (50/53) strains showed sensitivity for penicillins. We also identified β-lactamase activity among penicillin-resistant strains of S. canis. Clonal complex 13 (CC13) was detected only in lesions and formed independent clusters in the phylogenetic tree. One strain of CC13 was resistant to the anti-methicillin-resistant Staphylococcus aureus drugs, vancomycin and linezolid.
Conclusion
Although antibiotic-resistant strains of S. canis are isolated at a high rate, they can currently be treated with β-lactamase-inhibiting penicillins. CC13 may be a pathogenic cluster with high levels of antibiotics resistance.
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3
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Chochua S, Metcalf B, Li Z, Mathis S, Tran T, Rivers J, Fleming-Dutra KE, Li Y, McGee L, Beall B. Invasive Group A Streptococcal Penicillin Binding Protein 2× Variants Associated with Reduced Susceptibility to β-Lactam Antibiotics in the United States, 2015-2021. Antimicrob Agents Chemother 2022; 66:e0080222. [PMID: 35969070 PMCID: PMC9487518 DOI: 10.1128/aac.00802-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 07/18/2022] [Indexed: 11/20/2022] Open
Abstract
All known group A streptococci [GAS] are susceptible to β-lactam antibiotics. We recently identified an invasive GAS (iGAS) variant (emm43.4/PBP2x-T553K) with unusually high minimum inhibitory concentrations (MICs) for ampicillin and amoxicillin, although clinically susceptible to β-lactams. We aimed to quantitate PBP2x variants, small changes in β-lactam MICs, and lineages within contemporary population-based iGAS. PBP2x substitutions were comprehensively identified among 13,727 iGAS recovered during 2015-2021, in the USA. Isolates were subjected to antimicrobial susceptibility testing employing low range agar diffusion and PBP2x variants were subjected to phylogenetic analyses. Fifty-five variants were defined based upon substitutions within an assigned PBP2x transpeptidase domain. Twenty-nine of these variants, representing 338/13,727 (2.5%) isolates and 16 emm types, exhibited slightly elevated β-lactam MICs, none of which were above clinical breakpoints. The emm43.4/PBP2x-T553K variant, comprised of two isolates, displayed the most significant phenotype (ampicillin MIC 0.25 μg/ml) and harbored missense mutations within 3 non-PBP genes with known involvement in antibiotic efflux, membrane insertion of PBP2x, and peptidoglycan remodeling. The proportion of all PBP2x variants with elevated MICs remained stable throughout 2015-2021 (<3.0%). The predominant lineage (emm4/PBP2x-M593T/ermT) was resistant to macrolides/lincosamides and comprised 129/340 (37.9%) of isolates with elevated β-lactam MICs. Continuing β-lactam selective pressure is likely to have selected PBP2x variants that had escaped scrutiny due to MICs that remain below clinical cutoffs. Higher MICs exhibited by emm43.4/PBP2x-T553K are probably rare due to the requirement of additional mutations. Although elevated β-lactam MICs remain uncommon, emm43.4/PBP2x-T553K and emm4/PBP2x-M593T/ermT lineages indicate that antibiotic stewardship and strain monitoring is necessary.
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Affiliation(s)
- Sopio Chochua
- Respiratory Disease Branch, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Benjamin Metcalf
- Respiratory Disease Branch, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Zhongya Li
- ASRT Inc., Contractor to Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Saundra Mathis
- ASRT Inc., Contractor to Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Theresa Tran
- ASRT Inc., Contractor to Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Joy Rivers
- Respiratory Disease Branch, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Katherine E. Fleming-Dutra
- Respiratory Disease Branch, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Yuan Li
- Respiratory Disease Branch, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lesley McGee
- Respiratory Disease Branch, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Bernard Beall
- Respiratory Disease Branch, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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4
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Basu S, Varghese R, Debroy R, Ramaiah S, Veeraraghavan B, Anbarasu A. Non-steroidal anti-inflammatory drugs ketorolac and etodolac can augment the treatment against pneumococcal meningitis by targeting penicillin-binding proteins. Microb Pathog 2022; 170:105694. [DOI: 10.1016/j.micpath.2022.105694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 07/25/2022] [Accepted: 07/25/2022] [Indexed: 10/16/2022]
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5
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Chang B, Tamura K, Fujikura H, Watanabe H, Tanabe Y, Kuronuma K, Fujita J, Oshima K, Maruyama T, Abe S, Kasahara K, Nishi J, Kubota T, Kinjo Y, Serizawa Y, Shimbashi R, Fukusumi M, Shimada T, Sunagawa T, Suzuki M, Oishi K. Pneumococcal meningitis in adults in 2014-2018 after introduction of pediatric 13-valent pneumococcal conjugate vaccine in Japan. Sci Rep 2022; 12:3066. [PMID: 35197497 PMCID: PMC8866494 DOI: 10.1038/s41598-022-06950-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 02/09/2022] [Indexed: 12/04/2022] Open
Abstract
We assessed the impact of the pediatric 13-valent pneumococcal conjugate vaccine (PCV13) on pneumococcal meningitis in adults in Japan in 2014–2018 by comparing epidemiological characteristics of adults with invasive pneumococcal disease with (n = 222) and without (n = 1258) meningitis. The annual incidence of pneumococcal meningitis in 2016–2018 was 0.20–0.26 cases/100,000 population. Age (p < 0.001) and case fatality rate (p = 0.003) were significantly lower in patients with meningitis than in those without meningitis. The odds of developing meningitis were higher in asplenic/hyposplenic or splenectomized patients (adjusted odds ratio [aOR] 2.29, 95% CI 1.27–4.14), for serotypes 10A (aOR 3.26, 95% CI 2.10–5.06) or 23A (aOR 3.91, 95% CI 2.47–6.19), but lower for those aged ≥ 65 years (aOR 0.59, 95% CI 0.44–0.81). PCV13 had an indirect effect on nonmeningitis, but its impact on meningitis was limited because of an increase in non-PCV13 serotypes. Of meningitis isolates, 78 (35.1%) and 3 (1.4%) were penicillin G- or ceftriaxone-resistant, respectively. We also confirmed an association of the pbp1bA641C mutation with meningitis (aOR 2.92, 95% CI 1.51–5.65).
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Affiliation(s)
- Bin Chang
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kosuke Tamura
- Toyama Institute of Health, 17-1 Nakataiouyama, Imizu, Toyama, 939-0363, Japan
| | - Hiroyuki Fujikura
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan.,Center for Infectious Diseases, Nara Medical University, Nara, Japan
| | - Hiroshi Watanabe
- Department of Infection Control and Prevention, Kurume University School of Medicine, Kurume, Japan
| | - Yoshinari Tanabe
- Department of Respiratory Medicine, Niigata Prefectural Shibata Hospital, Niigata, Japan
| | - Koji Kuronuma
- Department of Respiratory Medicine and Allergology, Sapporo Medical University School of Medicine, Hokkaido, Japan
| | - Jiro Fujita
- Department of Infectious Diseases, Respiratory and Digestive Medicine, Faculty of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Kengo Oshima
- Department of Infectious Diseases, Tohoku University Hospital, Sendai, Miyagi, Japan
| | | | - Shuichi Abe
- Yamagata Prefectural Central Hospital, Yamagata, Japan
| | - Kei Kasahara
- Center for Infectious Diseases, Nara Medical University, Nara, Japan
| | - Junichiro Nishi
- Department of Microbiology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Tetsuya Kubota
- Department of Respiratory Medicine and Allergology, Kochi Medical School, Kochi University, Kochi, Japan
| | - Yuki Kinjo
- Department of Bacteriology, The Jikei University School of Medicine, Tokyo, Japan
| | - Yusuke Serizawa
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Reiko Shimbashi
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Munehisa Fukusumi
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tomoe Shimada
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tomimasa Sunagawa
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Motoi Suzuki
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kazunori Oishi
- Toyama Institute of Health, 17-1 Nakataiouyama, Imizu, Toyama, 939-0363, Japan.
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6
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Li L, Zhou J, Li M, Yu Z, Gao K, Yang J, Cheng P, Yang J, Zhang W, Yu Z, Sun H. Comparative Genomic Analysis of Streptococcus pneumoniae Strains: Penicillin Non-susceptible Multi-drug-Resistant Serotype 19A Isolates. Curr Microbiol 2022; 79:49. [PMID: 34982234 DOI: 10.1007/s00284-021-02715-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 11/11/2021] [Indexed: 11/03/2022]
Abstract
Streptococcus pneumoniae can cause several diseases including otitis media, sinusitis, pneumonia, sepsis and meningitis. The introduction of pneumococcal vaccines has changed the molecular epidemiological and antibiotic resistance profiles of related diseases. Analysis of molecular patterns and genome sequences of clinical strains may facilitate the identification of novel drug resistance mechanism. Three multidrug resistance 19A isolates were verified, serotyped and the complete genomes were sequenced combining the Pacific Biosciences and the Illumina Miseq platform. Genomic annotation revealed that similar central networks were found in the clinical isolates, and Mauve alignments indicated high similarity between different strains. The pan-genome analysis showed the shared and unique cluster in the strains. Mobile elements were predicted in the isolates including prophages and CRISPER systems, which may participate in the virulence and antibiotic resistance of the strains. The presence of 31 virulence factor genes was predicted from other pathogens for PRSP 19339 and 19343, while 30 for PRSP 19087. Meanwhile, 33 genes antibiotic resistance genes were predicted including antibiotic resistance genes, antibiotic-target genes and antibiotic biosynthesis genes. Further analysis of the antibiotic resistance genes revealed new mutations in the isolates. By comparative genomic analysis, we contributed to the understanding of resistance mechanism of the clinical isolates with other serotype strains, which could facilitate the concrete drug resistance mechanism study.
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Affiliation(s)
- Lifeng Li
- Henan Neurodevelopment Engineering Research Center for Children, Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated To Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China.,Departments of Neonatology, Children's Hospital Affiliated To Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China
| | - Juanjuan Zhou
- Zhengzhou Key Laboratory of Children's Infection and Immunity, Department of Laboratory Medicine, Children's Hospital Affiliated To Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China
| | - Mingchao Li
- Departments of Neonatology, Children's Hospital Affiliated To Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China
| | - Zengyuan Yu
- Departments of Neonatology, Children's Hospital Affiliated To Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China
| | - Kaijie Gao
- Zhengzhou Key Laboratory of Children's Infection and Immunity, Department of Laboratory Medicine, Children's Hospital Affiliated To Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China
| | - Junwen Yang
- Zhengzhou Key Laboratory of Children's Infection and Immunity, Department of Laboratory Medicine, Children's Hospital Affiliated To Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China
| | - Ping Cheng
- Departments of Neonatology, Children's Hospital Affiliated To Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China
| | - Junmei Yang
- Zhengzhou Key Laboratory of Children's Infection and Immunity, Department of Laboratory Medicine, Children's Hospital Affiliated To Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China.
| | - Wancun Zhang
- Henan Neurodevelopment Engineering Research Center for Children, Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated To Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China.
| | - Zhidan Yu
- Henan Neurodevelopment Engineering Research Center for Children, Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated To Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China.
| | - Huiqing Sun
- Departments of Neonatology, Children's Hospital Affiliated To Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China.
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7
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Bamphensin N, Chopjitt P, Hatrongjit R, Boueroy P, Fittipaldi N, Gottschalk M, Kerdsin A. Non-Penicillin-Susceptible Streptococcus suis Isolated from Humans. Pathogens 2021; 10:pathogens10091178. [PMID: 34578210 PMCID: PMC8471365 DOI: 10.3390/pathogens10091178] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/07/2021] [Accepted: 09/10/2021] [Indexed: 11/16/2022] Open
Abstract
Streptococcus suis is a pathogen that causes invasive infections in humans and pigs. In this study, 448 S. suis isolates recovered from human infections in Thailand were characterized with regard to their antimicrobial susceptibility and antimicrobial resistance genes, including, for non-penicillin-susceptible isolates, sequence analyses of five genes encoding penicillin-binding proteins (pbp1a, pbp1b, pbp2a, pbp2b, and pbp2x). All 448 isolates were susceptible to cefepime and ceftriaxone, whereas 99.6%, 91.7%, and 72.9% of the isolates were susceptible to levofloxacin, penicillin, and chloramphenicol, respectively. Almost all isolates were resistant to tetracycline (98.2%), clindamycin (94%), erythromycin (92.4%), and azithromycin (82.6%). Genes tet(O) and ermB were the predominant resistance genes detected among macrolide- and tetracycline-resistant isolates. A total of 37 out of 448 isolates (8.2%) showed intermediately resistance to penicillin. Most of these isolates (59.5%) belonged to serotype 2-ST233. Comparison of the predicted translated sequences of five PBP proteins of a penicillin-susceptible isolate (strain P1/7) to the respective PBP sequences of ten non-penicillin-susceptible isolates revealed multiple amino acid substitutions. Isolates of CC221/234 showed highly variable amino acid substitutions in all PBP proteins. An ST104 isolate had a higher number of amino acid substitutions in PBP2X. Isolates belonging to CC233/379 had numerous substitutions in PBP2B and PBP2X. ST25 isolates exhibited fewer amino acid substitutions than isolates of other STs in all five PBPs. The antimicrobial resistance of S. suis is increasing worldwide; therefore, restrictions on antimicrobial use, continuous control, and the surveillance of this bacterium throughout the pork supply chain are crucial for ensuring public health and must be a priority concern.
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Affiliation(s)
- Nichari Bamphensin
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon 47000, Thailand; (N.B.); (P.C.); (P.B.)
| | - Peechanika Chopjitt
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon 47000, Thailand; (N.B.); (P.C.); (P.B.)
| | - Rujirat Hatrongjit
- Department of General Sciences, Faculty of Science and Engineering, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon 47000, Thailand;
| | - Parichart Boueroy
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon 47000, Thailand; (N.B.); (P.C.); (P.B.)
| | - Nahuel Fittipaldi
- GREMIP, Faculty of Veterinary Medicine, University of Montreal, Montreal, QC H3T 1J4, Canada; (N.F.); (M.G.)
| | - Marcelo Gottschalk
- GREMIP, Faculty of Veterinary Medicine, University of Montreal, Montreal, QC H3T 1J4, Canada; (N.F.); (M.G.)
| | - Anusak Kerdsin
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon 47000, Thailand; (N.B.); (P.C.); (P.B.)
- Correspondence: ; Tel.: +66-42-725-025
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8
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Hadjirin NF, Miller EL, Murray GGR, Yen PLK, Phuc HD, Wileman TM, Hernandez-Garcia J, Williamson SM, Parkhill J, Maskell DJ, Zhou R, Fittipaldi N, Gottschalk M, Tucker AW(D, Hoa NT, Welch JJ, Weinert LA. Large-scale genomic analysis of antimicrobial resistance in the zoonotic pathogen Streptococcus suis. BMC Biol 2021; 19:191. [PMID: 34493269 PMCID: PMC8422772 DOI: 10.1186/s12915-021-01094-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 07/13/2021] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) is among the gravest threats to human health and food security worldwide. The use of antimicrobials in livestock production can lead to emergence of AMR, which can have direct effects on humans through spread of zoonotic disease. Pigs pose a particular risk as they are a source of zoonotic diseases and receive more antimicrobials than most other livestock. Here we use a large-scale genomic approach to characterise AMR in Streptococcus suis, a commensal found in most pigs, but which can also cause serious disease in both pigs and humans. RESULTS We obtained replicated measures of Minimum Inhibitory Concentration (MIC) for 16 antibiotics, across a panel of 678 isolates, from the major pig-producing regions of the world. For several drugs, there was no natural separation into 'resistant' and 'susceptible', highlighting the need to treat MIC as a quantitative trait. We found differences in MICs between countries, consistent with their patterns of antimicrobial usage. AMR levels were high even for drugs not used to treat S. suis, with many multidrug-resistant isolates. Similar levels of resistance were found in pigs and humans from regions associated with zoonotic transmission. We next used whole genome sequences for each isolate to identify 43 candidate resistance determinants, 22 of which were novel in S. suis. The presence of these determinants explained most of the variation in MIC. But there were also interesting complications, including epistatic interactions, where known resistance alleles had no effect in some genetic backgrounds. Beta-lactam resistance involved many core genome variants of small effect, appearing in a characteristic order. CONCLUSIONS We present a large dataset allowing the analysis of the multiple contributing factors to AMR in S. suis. The high levels of AMR in S. suis that we observe are reflected by antibiotic usage patterns but our results confirm the potential for genomic data to aid in the fight against AMR.
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Affiliation(s)
- Nazreen F. Hadjirin
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Eric L. Miller
- grid.256868.70000 0001 2215 7365Microbial Ecology and Evolution Laboratory, Haverford College, Haverford, USA
| | - Gemma G. R. Murray
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Phung L. K. Yen
- grid.412433.30000 0004 0429 6814Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ho D. Phuc
- grid.412433.30000 0004 0429 6814Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Thomas M. Wileman
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Juan Hernandez-Garcia
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Susanna M. Williamson
- grid.13689.350000 0004 0426 1697Department for Environment, Food and Rural Affairs (Defra), London, UK
| | - Julian Parkhill
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Duncan J. Maskell
- grid.1008.90000 0001 2179 088XChancellery, University of Melbourne, Melbourne, Australia
| | - Rui Zhou
- grid.35155.370000 0004 1790 4137College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Nahuel Fittipaldi
- grid.14848.310000 0001 2292 3357Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, Canada
| | - Marcelo Gottschalk
- grid.14848.310000 0001 2292 3357Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, Canada
| | - A. W. ( Dan) Tucker
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Ngo Thi Hoa
- grid.412433.30000 0004 0429 6814Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - John J. Welch
- grid.5335.00000000121885934Department of Genetics, University of Cambridge, Cambridge, UK
| | - Lucy A. Weinert
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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9
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Peters K, Schweizer I, Hakenbeck R, Denapaite D. New Insights into Beta-Lactam Resistance of Streptococcus pneumoniae: Serine Protease HtrA Degrades Altered Penicillin-Binding Protein 2x. Microorganisms 2021; 9:microorganisms9081685. [PMID: 34442764 PMCID: PMC8400419 DOI: 10.3390/microorganisms9081685] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 08/02/2021] [Accepted: 08/04/2021] [Indexed: 11/18/2022] Open
Abstract
Reduced amounts of the essential penicillin-binding protein 2x (PBP2x) were detected in two cefotaxime-resistant Streptococcus pneumoniae laboratory mutants C405 and C606. These mutants contain two or four mutations in the penicillin-binding domain of PBP2x, respectively. The transcription of the pbp2x gene was not affected in both mutants; thus, the reduced PBP2x amounts were likely due to post-transcriptional regulation. The mutants carry a mutation in the histidine protein kinase gene ciaH, resulting in enhanced gene expression mediated by the cognate response regulator CiaR. Deletion of htrA, encoding a serine protease regulated by CiaR, or inactivation of HtrA proteolytic activity showed that HtrA is indeed responsible for PBP2x degradation in both mutants, and that this affects β-lactam resistance. Depletion of the PBP2xC405 in different genetic backgrounds confirmed that HtrA degrades PBP2xC405. A GFP-PBP2xC405 fusion protein still localized at the septum in the absence of HtrA. The complementation studies in HtrA deletion strains showed that HtrA can be overexpressed in pneumococcal cells to specific levels, depending on the genetic background. Quantitative Western blotting revealed that the PBP2x amount in C405 strain was less than 20% compared to parental strain, suggesting that PBP2x is an abundant protein in S. pneumoniae R6 strain.
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10
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Varghese R, Veeraraghavan B. Decoding the Penicillin Resistance of Streptococcus pneumoniae for Invasive and Noninvasive Infections. Microb Drug Resist 2021; 27:942-950. [DOI: 10.1089/mdr.2020.0233] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Rosemol Varghese
- Department of Clinical Microbiology, Christian Medical College, Vellore, India
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11
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Comparative genomics of invasive Streptococcus pneumoniae CC320/271 serotype 19F/19A before the introduction of pneumococcal vaccine in India. Mol Biol Rep 2021; 48:3265-3276. [PMID: 33876375 DOI: 10.1007/s11033-021-06353-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 04/12/2021] [Indexed: 10/21/2022]
Abstract
The emergence of multi drug resistant clone CC320 serotype19F/19A and their capsular (cps) antigenic variants due to selective pressures such as vaccine had been reported worldwide. Hence, it is important to identify the prevalent clones, sequence types and cps variants of serotype 19F/19A in India, where PCV13 has been recently introduced. Multi-locus sequence typing (MLST) was performed for all (n = 21) invasive S. pneumoniae isolates of serotype 19A (n = 5) and 19F (n = 16) collected between the years 2012 and 2018 from children less than 5 years. The genome characterization by whole genome sequencing for the Sequence types (STs) 320 and 271(n = 7) were performed and compared with another six Indian WGSs of similar STs available from the GPS platform. The predominant STs in the serotype 19F/19A study isolates were of CC320: ST 320, 236 and 271, associated with PMEN clone Taiwan19F-14. The WGSs of CC320 study isolates showed high genomic similarity to the Taiwan19F-14 clone, and the penicillin binding protein (PBP) amino acid sequence similarity was 100% for PBP1A, 93% for PBP 2B and 2X. Whilst PBP comparison with other global MDR ST320 strains revealed that the ST320 clones in India are of low-level penicillin resistance. The presence of a few ST320/19A/19F invasive isolates with high similarity to the Taiwan clone suggests slow and gradual expansion of Taiwan19F-14 associated CC320 clones in India. Since serotype 19F/19A is covered by PCV13 vaccine, the expansion of 19F/19A cones with non-PCV13 vaccine serotype in India should be monitored.
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12
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Chaguza C, Senghore M, Bojang E, Gladstone RA, Lo SW, Tientcheu PE, Bancroft RE, Worwui A, Foster-Nyarko E, Ceesay F, Okoi C, McGee L, Klugman KP, Breiman RF, Barer MR, Adegbola RA, Antonio M, Bentley SD, Kwambana-Adams BA. Within-host microevolution of Streptococcus pneumoniae is rapid and adaptive during natural colonisation. Nat Commun 2020; 11:3442. [PMID: 32651390 PMCID: PMC7351774 DOI: 10.1038/s41467-020-17327-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 06/25/2020] [Indexed: 02/08/2023] Open
Abstract
Genomic evolution, transmission and pathogenesis of Streptococcus pneumoniae, an opportunistic human-adapted pathogen, is driven principally by nasopharyngeal carriage. However, little is known about genomic changes during natural colonisation. Here, we use whole-genome sequencing to investigate within-host microevolution of naturally carried pneumococci in ninety-eight infants intensively sampled sequentially from birth until twelve months in a high-carriage African setting. We show that neutral evolution and nucleotide substitution rates up to forty-fold faster than observed over longer timescales in S. pneumoniae and other bacteria drives high within-host pneumococcal genetic diversity. Highly divergent co-existing strain variants emerge during colonisation episodes through real-time intra-host homologous recombination while the rest are co-transmitted or acquired independently during multiple colonisation episodes. Genic and intergenic parallel evolution occur particularly in antibiotic resistance, immune evasion and epithelial adhesion genes. Our findings suggest that within-host microevolution is rapid and adaptive during natural colonisation.
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Affiliation(s)
- Chrispin Chaguza
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- Darwin College, University of Cambridge, Silver Street, Cambridge, UK.
| | - Madikay Senghore
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Ebrima Bojang
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Rebecca A Gladstone
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Stephanie W Lo
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Peggy-Estelle Tientcheu
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Rowan E Bancroft
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Archibald Worwui
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Ebenezer Foster-Nyarko
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Fatima Ceesay
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Catherine Okoi
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Lesley McGee
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, USA
| | - Keith P Klugman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, USA
| | | | - Michael R Barer
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, UK
| | - Richard A Adegbola
- RAMBICON Immunisation & Global Health Consulting, 6A Platinum Close, Lekki, Lagos State, Nigeria
| | - Martin Antonio
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Stephen D Bentley
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- Department of Pathology, University of Cambridge, Cambridge, UK.
| | - Brenda A Kwambana-Adams
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia.
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK.
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13
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McDougall S, Clausen L, Ha HJ, Gibson I, Bryan M, Hadjirin N, Lay E, Raisen C, Ba X, Restif O, Parkhill J, Holmes MA. Mechanisms of β-lactam resistance of Streptococcus uberis isolated from bovine mastitis cases. Vet Microbiol 2020; 242:108592. [PMID: 32122596 DOI: 10.1016/j.vetmic.2020.108592] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 01/12/2020] [Accepted: 01/21/2020] [Indexed: 11/24/2022]
Abstract
A number of veterinary clinical pathology laboratories in New Zealand have been reporting emergence of increased minimum in inhibitory concentrations for β-lactams in the common clinical bovine mastitis pathogen Streptococcus uberis. The objective of this study was to determine the genetic basis of this increase in MIC for β-lactams amongst S. uberis. Illumina sequencing and determination of oxacillin MIC was performed on 265 clinical isolates. Published sequences of the five penicillin binding proteins pbp1a, pbp1b, pbp2a, pbp2b, and pbp2x were used to identify, extract and align these sequences from the study isolates. Amino acid substitutions resulting from single nucleotide polymorphisms (SNP) within these genes were analysed for associations with elevated (≥ 0.5 mg/L) oxacillin MIC together with a genome wide association study. The population structure of the study isolates was approximated using a phylogenetic tree generated from an alignment of the core genome. A total of 53 % of isolates had MIC ≥ 0.5 mg/L for oxacillin. A total of 101 substitutions within the five pbp were identified, of which 11 were statistically associated with an MIC ≥ 0.5 mg/L. All 140 isolates which exhibited an increased β-lactam MIC had SNPs leading to pbp2x E381K and Q554E substitutions. The phylogenetic tree indicated that the genotype and phenotype associated with the increased MIC for oxacillin were present in several different lineages suggesting that acquisition of this increased β-lactam MIC had occurred in multiple geographically distinct regions. Reanalysis of the data from the intervention studies from which the isolates were originally drawn found a tendency for the pbp2x E381K substitution to be associated with lower cure rates. It is concluded that there is geographically and genetically widespread presence of pbp substitutions associated with reduced susceptibility to β-lactam antimicrobials. Additionally, presence of pbp substitutions tended to be associated with poorer cure rate outcomes following antimicrobial therapy for clinical mastitis.
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Affiliation(s)
| | | | - Hye-Jeong Ha
- Animal Health Laboratory, Ministry for Primary Industry, Upper Hutt, New Zealand
| | - Isobel Gibson
- New Zealand Veterinary Pathology, Hamilton, New Zealand
| | | | - Nazreen Hadjirin
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK
| | - Elizabeth Lay
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK
| | - Claire Raisen
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK
| | - Xiaoliang Ba
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK
| | - Olivier Restif
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK; Wellcome Sanger Institute, Hinxton, UK
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK
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14
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He JX, Le Mai Hoang K, Kho SH, Guo Z, Zhong W, Venkata Thappeta KR, Zamudio-Vázquez R, Hoo SN, Xiong Q, Duan H, Yang L, Chan-Park MB, Liu XW. Synthetic biohybrid peptidoglycan oligomers enable pan-bacteria-specific labeling and imaging: in vitro and in vivo. Chem Sci 2020; 11:3171-3179. [PMID: 34122822 PMCID: PMC8157403 DOI: 10.1039/c9sc06345e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Peptidoglycan is the core component of the bacterial cell wall, which makes it an attractive target for the development of bacterial targeting agents. Intercepting its enzymatic assembly with synthetic substrates allows for labeling and engineering of live bacterial cells. Over the past two decades, small-molecule-based labeling agents, such as antibiotics, d-amino acids or monosaccharides have been developed for probing biological processes in bacteria. Herein, peptidoglycan oligomers, substrates for transglycosylation, are prepared for the first time using a top-down approach, which starts from chitosan as a cheap feedstock. A high efficiency of labeling has been observed in all bacterial strains tested using micromolar substrates. In contrast, uptake into mammalian cells was barely observable. Additional mechanistic studies support a hypothesis of bacteria-specific metabolic labeling rather than non-specific binding to the bacterial surface. Eventually, its practicality in bacterial targeting capability is demonstrated in resistant strain detection and in vivo infection models.
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Affiliation(s)
- Jing-Xi He
- School of Physical and Mathematical Sciences, Nanyang Technological University 21 Nanyang Link Singapore 637371 Singapore .,School of Chemical and Biomedical Engineering, Nanyang Technological University 62 Nanyang Drive Singapore 637459 Singapore
| | - Kim Le Mai Hoang
- School of Physical and Mathematical Sciences, Nanyang Technological University 21 Nanyang Link Singapore 637371 Singapore
| | - Shu Hui Kho
- School of Physical and Mathematical Sciences, Nanyang Technological University 21 Nanyang Link Singapore 637371 Singapore .,NTU Institute for Health Technologies, Nanyang Technological University Singapore
| | - Zhong Guo
- School of Physical and Mathematical Sciences, Nanyang Technological University 21 Nanyang Link Singapore 637371 Singapore
| | - Wenbin Zhong
- School of Chemical and Biomedical Engineering, Nanyang Technological University 62 Nanyang Drive Singapore 637459 Singapore
| | - Kishore Reddy Venkata Thappeta
- School of Chemical and Biomedical Engineering, Nanyang Technological University 62 Nanyang Drive Singapore 637459 Singapore
| | - Rubí Zamudio-Vázquez
- School of Chemical and Biomedical Engineering, Nanyang Technological University 62 Nanyang Drive Singapore 637459 Singapore
| | - Sin Ni Hoo
- School of Physical and Mathematical Sciences, Nanyang Technological University 21 Nanyang Link Singapore 637371 Singapore
| | - Qirong Xiong
- School of Chemical and Biomedical Engineering, Nanyang Technological University 62 Nanyang Drive Singapore 637459 Singapore
| | - Hongwei Duan
- School of Chemical and Biomedical Engineering, Nanyang Technological University 62 Nanyang Drive Singapore 637459 Singapore
| | - Liang Yang
- School of Medicine, Southern University of Science and Technology Shenzhen 518055 China
| | - Mary B Chan-Park
- School of Chemical and Biomedical Engineering, Nanyang Technological University 62 Nanyang Drive Singapore 637459 Singapore
| | - Xue-Wei Liu
- School of Physical and Mathematical Sciences, Nanyang Technological University 21 Nanyang Link Singapore 637371 Singapore
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15
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Lau CHF, DeJong EN, Dussault F, Carrillo C, Stogios PJ, Savchenko A, Topp E. A penicillin-binding protein that can promote advanced-generation cephalosporin resistance and genome adaptation in the opportunistic pathogen Pseudomonas aeruginosa. Int J Antimicrob Agents 2020; 55:105896. [PMID: 31927042 DOI: 10.1016/j.ijantimicag.2020.105896] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 12/16/2019] [Accepted: 01/04/2020] [Indexed: 11/28/2022]
Abstract
A previous soil metagenomics study recovered a novel cephalosporin resistance determinant, pbpTET A6, for which the exact resistance mechanism was unclear. This study used a three-dimensional structure-guided mutagenesis approach to demonstrate that PBPTET A6 is likely to be a class A penicillin-binding protein (PBP), and that its ability to confer cephalosporin resistance is directly linked to the functional integrity of its transpeptidase (TP) catalytic core. Screening of a library of PBPTET A6 variants carrying randomly introduced point mutations revealed additional residue modifications that compromised resistance, all of which were proximal to the TP active site except one which was found in a 29-amino-acid-long superstructure (α6-α7 loop) absent in other class A PBP homologues. Based on the site-specific mutagenesis results, it is hypothesized that residue arginine-400 plays an important role in limiting the access of certain cephalosporin compounds to the enzymatic core of the TP domain of PBPTET A6. Using a combination of adaptive evolution assays and whole-genome sequencing, the potential impact of PBPTET A6 on promoting the development of resistance in the clinically significant opportunistic pathogen Pseudomonas aeruginosa was investigated. Under the selective pressure of serial ceftazidime exposures, the pbpTET A6-expressing P. aeruginosa population readily evolved by excluding a ~400-kbp chromosomal element to acquire additional resistance against cephalosporins, suggesting that PBPTET A6 has a catalytic effect on facilitating antibiotic-resistance-associated genome adaptation. Overall, the soil environment contains genes conferring resistance to critically important antibiotics by cryptic mechanisms. Understanding what impact anthropogenic activities might have on the abundance and evolution of these genes should be a priority.
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Affiliation(s)
- Calvin Ho-Fung Lau
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario, Canada; Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, Ontario, Canada.
| | - Erica N DeJong
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario, Canada
| | - Forest Dussault
- Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, Ontario, Canada
| | - Catherine Carrillo
- Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, Ontario, Canada
| | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada; Center for Structural Genomics of Infectious Diseases
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada; Center for Structural Genomics of Infectious Diseases; Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Edward Topp
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario, Canada; Department of Biology, University of Western Ontario, London, Ontario, Canada.
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16
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Veeraraghavan B, Walia K. Antimicrobial susceptibility profile & resistance mechanisms of Global Antimicrobial Resistance Surveillance System (GLASS) priority pathogens from India. Indian J Med Res 2019; 149:87-96. [PMID: 31219073 PMCID: PMC6563747 DOI: 10.4103/ijmr.ijmr_214_18] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Antimicrobial resistance is a major concern globally. Infections due to drug-resistant pathogens are becoming difficult and a challenge to treat. As treatment choices are limited due to the high-drug resistance rates, there is an increase in the health care cost, duration of hospital stay, morbidity and mortality rates. Understanding the true burden of antimicrobial resistance for a geographical location is important to guide effective empirical therapy. To have a national data, it is imperative to have a systemic data capturing across the country through surveillance studies. Very few surveillance studies have been conducted in India to generate national data on antimicrobial resistance. This review aims to report the cumulative antibiogram and the resistance mechanisms of Global Antimicrobial Resistance Surveillance System (GLASS) priority pathogens from India.
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Affiliation(s)
| | - Kamini Walia
- Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi, India
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17
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Ealand CS, Machowski EE, Kana BD. β-lactam resistance: The role of low molecular weight penicillin binding proteins, β-lactamases and ld-transpeptidases in bacteria associated with respiratory tract infections. IUBMB Life 2018; 70:855-868. [PMID: 29717815 DOI: 10.1002/iub.1761] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 04/04/2018] [Indexed: 02/02/2023]
Abstract
Disruption of peptidoglycan (PG) biosynthesis in the bacterial cell wall by β-lactam antibiotics has transformed therapeutic options for bacterial infections. These antibiotics target the transpeptidase domains in penicillin binding proteins (PBPs), which can be classified into high and low molecular weight (LMW) counterparts. While the essentiality of the former has been extensively demonstrated, the physiological roles of LMW PBPs remain poorly understood. Herein, we review the function of LMW PBPs, β-lactamases and ld-transpeptidases (Ldts) in pathogens associated with respiratory tract infections. More specifically, we explore their roles in mediating β-lactam resistance. Using a comparative genomics approach, we identified a high degree of genetic redundancy for LMW PBPs which retain the motifs, SxxN, SxN and KTG required for catalytic activity. Differences in domain architecture suggest distinct physiological roles, possibly related to bacterial cell cycle and/or adaptation to various environmental conditions. Many of the LMW PBPs play an important role in β-lactam resistance either through mutation or variation in abundance. In all of the bacterial genomes assessed, at least one β-lactamase homologue is present, suggesting that enzymatic degradation of β-lactams is a highly conserved resistance mechanism. Furthermore, the presence of Ldt homologues in the majority of species surveyed suggests that alternative PG crosslinking may further mediate β-lactam drug resistance. A deeper understanding of the interplay between these different mechanisms of β-lactam resistance will provide a framework for new therapeutics, which are urgently required given the rapid emergence of antimicrobial resistance. © 2018 IUBMB Life, 70(9):855-868, 2018.
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Affiliation(s)
- Christopher S Ealand
- DST/NRF Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
| | - Edith E Machowski
- DST/NRF Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
| | - Bavesh D Kana
- DST/NRF Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa.,MRC-CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Centre for the AIDS Programme of Research in South Africa, CAPRISA, Durban, South Africa
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18
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Jindal HM, Ramanathan B, Le CF, Gudimella R, Razali R, Manikam R, Sekaran SD. Comparative genomic analysis of ten clinical Streptococcus pneumoniae collected from a Malaysian hospital reveal 31 new unique drug-resistant SNPs using whole genome sequencing. J Biomed Sci 2018; 25:15. [PMID: 29448938 PMCID: PMC5815235 DOI: 10.1186/s12929-018-0414-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 01/29/2018] [Indexed: 11/30/2022] Open
Abstract
Background Streptococcus pneumoniae or pneumococcus is a leading cause of morbidity and mortality worldwide, specifically in relation to community-acquired pneumonia. Due to the overuse of antibiotics, S. pneumoniae has developed a high degree of resistance to a wide range of antibacterial drugs. Methods In this study, whole genome sequencing (WGS) was performed for 10 clinical strains of S. pneumoniae with different levels of sensitivity to standard antibiotics. The main objective was to investigate genetic changes associated with antibiotic resistance in S. pneumoniae. Results Our results showed that resistant isolates contain a higher number of non-synonymous single nucleotide polymorphisms (SNPs) as compared to susceptible isolates. We were able to identify SNPs that alter a single amino acid in many genes involved in virulence and capsular polysaccharide synthesis. In addition, 90 SNPs were only presented in the resistant isolates, and 31 SNPs were unique and had not been previously reported, suggesting that these unique SNPs could play a key role in altering the level of resistance to different antibiotics. Conclusion Whole genome sequencing is a powerful tool for comparing the full genome of multiple isolates, especially those closely related, and for analysing the variations found within antibiotic resistance genes that lead to differences in antibiotic sensitivity. We were able to identify specific mutations within virulence genes related to resistant isolates. These findings could provide insights into understanding the role of single nucleotide mutants in conferring drug resistance. Electronic supplementary material The online version of this article (10.1186/s12929-018-0414-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hassan Mahmood Jindal
- Department of Medical Microbiology, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Babu Ramanathan
- Department of Biological Sciences, School of Science and Technology, Sunway University, 47500, Kuala Lumpur, Malaysia
| | - Cheng Foh Le
- School of Pharmacy, University of Nottingham Malaysia Campus, 43500, Semenyih, Selangor, Malaysia
| | | | - Rozaimi Razali
- Sengenics HIR, University Malaya, 50603, Kuala Lumpur, Malaysia
| | - Rishya Manikam
- Department of Trauma and Emergency, University Malaya Medical Centre, 50603, Kuala Lumpur, Malaysia
| | - Shamala Devi Sekaran
- Department of Microbiology, Faculty of Medicine, MAHSA University, 42610, Jenjarom, Malaysia.
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19
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Cephalosporin-NO-donor prodrug PYRRO-C3D shows β-lactam - mediated activity against Streptococcus pneumoniae biofilms. Nitric Oxide 2017; 65:43-49. [DOI: 10.1016/j.niox.2017.02.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 02/06/2017] [Accepted: 02/16/2017] [Indexed: 11/21/2022]
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20
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Makarewicz O, Lucas M, Brandt C, Herrmann L, Albersmeier A, Rückert C, Blom J, Goesmann A, van der Linden M, Kalinowski J, Pletz MW. Whole Genome Sequencing of 39 Invasive Streptococcus pneumoniae Sequence Type 199 Isolates Revealed Switches from Serotype 19A to 15B. PLoS One 2017; 12:e0169370. [PMID: 28046133 PMCID: PMC5207522 DOI: 10.1371/journal.pone.0169370] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 12/15/2016] [Indexed: 11/18/2022] Open
Abstract
Streptococcus pneumoniae is a major pathogen that causes different invasive pneumococcal diseases (IPD). The pneumococcal polysaccharide capsule is a main virulence factor. More than 94 capsule types have been described, but only a limited number of capsule types accounted for the majority of IPD cases before the introduction of pneumococcal vaccines. After the introduction of the conjugated pneumococcal vaccine PCV7, which covered the seven most frequent serotypes in IPD in the USA, an increase in IPD caused by non-vaccine serotypes was observed, and serotype 19A, which belongs to sequence type (ST) 199, was among the most prevalent STs. After the introduction of the extended vaccine PCV13, which includes serotype 19A, serogroup 15B/C increased in IPD. Therefore, whole genome sequences of 39 isolates of ST199 from Germany (collected between 1998 and 2011) with serotype 19A (n = 24) and serogroup 15B/C (n = 15) were obtained using an Illumina platform and were analysed to identify capsular switches within ST199. Two 19A to 15B/C serotype switch events were identified. Both events occurred before the introduction of PCV7, which indicates that a capsular switch from 19A to 15B among ST199 isolates is not unusual and is not directly linked to the vaccination. The observed serotype replacement appears to be the result of a vacant niche due to the displacement of vaccine serotypes that is now successfully occupied by ST199 clones.
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Affiliation(s)
- Oliwia Makarewicz
- Center for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
- * E-mail:
| | - Marie Lucas
- Center for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
| | - Christian Brandt
- Center for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
| | - Leonie Herrmann
- Center for Biotechology, University of Bielefeld, Bielefeld, Germany
| | | | - Christian Rückert
- Center for Biotechology, University of Bielefeld, Bielefeld, Germany
| | - Jochen Blom
- Institute for Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Alexander Goesmann
- Institute for Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Mark van der Linden
- German National Reference Center of Streptococci, University Hospital RWTH Aachen, Aachen, Germany
| | - Jörn Kalinowski
- Center for Biotechology, University of Bielefeld, Bielefeld, Germany
| | - Mathias W. Pletz
- Center for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
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21
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van Opijnen T, Dedrick S, Bento J. Strain Dependent Genetic Networks for Antibiotic-Sensitivity in a Bacterial Pathogen with a Large Pan-Genome. PLoS Pathog 2016; 12:e1005869. [PMID: 27607357 PMCID: PMC5015961 DOI: 10.1371/journal.ppat.1005869] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/15/2016] [Indexed: 11/19/2022] Open
Abstract
The interaction between an antibiotic and bacterium is not merely restricted to the drug and its direct target, rather antibiotic induced stress seems to resonate through the bacterium, creating selective pressures that drive the emergence of adaptive mutations not only in the direct target, but in genes involved in many different fundamental processes as well. Surprisingly, it has been shown that adaptive mutations do not necessarily have the same effect in all species, indicating that the genetic background influences how phenotypes are manifested. However, to what extent the genetic background affects the manner in which a bacterium experiences antibiotic stress, and how this stress is processed is unclear. Here we employ the genome-wide tool Tn-Seq to construct daptomycin-sensitivity profiles for two strains of the bacterial pathogen Streptococcus pneumoniae. Remarkably, over half of the genes that are important for dealing with antibiotic-induced stress in one strain are dispensable in another. By confirming over 100 genotype-phenotype relationships, probing potassium-loss, employing genetic interaction mapping as well as temporal gene-expression experiments we reveal genome-wide conditionally important/essential genes, we discover roles for genes with unknown function, and uncover parts of the antibiotic's mode-of-action. Moreover, by mapping the underlying genomic network for two query genes we encounter little conservation in network connectivity between strains as well as profound differences in regulatory relationships. Our approach uniquely enables genome-wide fitness comparisons across strains, facilitating the discovery that antibiotic responses are complex events that can vary widely between strains, which suggests that in some cases the emergence of resistance could be strain specific and at least for species with a large pan-genome less predictable.
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Affiliation(s)
- Tim van Opijnen
- Boston College, Biology Department, Chestnut Hill, Massachusetts, United States of America
| | - Sandra Dedrick
- Boston College, Biology Department, Chestnut Hill, Massachusetts, United States of America
| | - José Bento
- Boston College, Computer Science Department, Massachusetts, United States of America
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Kim L, McGee L, Tomczyk S, Beall B. Biological and Epidemiological Features of Antibiotic-Resistant Streptococcus pneumoniae in Pre- and Post-Conjugate Vaccine Eras: a United States Perspective. Clin Microbiol Rev 2016; 29:525-52. [PMID: 27076637 PMCID: PMC4861989 DOI: 10.1128/cmr.00058-15] [Citation(s) in RCA: 169] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Streptococcus pneumoniae inflicts a huge disease burden as the leading cause of community-acquired pneumonia and meningitis. Soon after mainstream antibiotic usage, multiresistant pneumococcal clones emerged and disseminated worldwide. Resistant clones are generated through adaptation to antibiotic pressures imposed while naturally residing within the human upper respiratory tract. Here, a huge array of related commensal streptococcal strains transfers core genomic and accessory resistance determinants to the highly transformable pneumococcus. β-Lactam resistance is the hallmark of pneumococcal adaptability, requiring multiple independent recombination events that are traceable to nonpneumococcal origins and stably perpetuated in multiresistant clonal complexes. Pneumococcal strains with elevated MICs of β-lactams are most often resistant to additional antibiotics. Basic underlying mechanisms of most pneumococcal resistances have been identified, although new insights that increase our understanding are continually provided. Although all pneumococcal infections can be successfully treated with antibiotics, the available choices are limited for some strains. Invasive pneumococcal disease data compiled during 1998 to 2013 through the population-based Active Bacterial Core surveillance program (U.S. population base of 30,600,000) demonstrate that targeting prevalent capsular serotypes with conjugate vaccines (7-valent and 13-valent vaccines implemented in 2000 and 2010, respectively) is extremely effective in reducing resistant infections. Nonetheless, resistant non-vaccine-serotype clones continue to emerge and expand.
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Affiliation(s)
- Lindsay Kim
- Epidemiology Section, Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lesley McGee
- Streptococcus Laboratory, Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sara Tomczyk
- Epidemiology Section, Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Bernard Beall
- Streptococcus Laboratory, Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Microscale insights into pneumococcal antibiotic mutant selection windows. Nat Commun 2015; 6:8773. [PMID: 26514094 PMCID: PMC4632196 DOI: 10.1038/ncomms9773] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 09/30/2015] [Indexed: 11/26/2022] Open
Abstract
The human pathogen Streptococcus pneumoniae shows alarming rates of antibiotic resistance emergence. The basic requirements for de novo resistance emergence are poorly understood in the pneumococcus. Here we systematically analyse the impact of antibiotics on S. pneumoniae at concentrations that inhibit wild type cells, that is, within the mutant selection window. We identify discrete growth-inhibition profiles for bacteriostatic and bactericidal compounds, providing a predictive framework for distinction between the two classifications. Cells treated with bacteriostatic agents show continued gene expression activity, and real-time mutation assays link this activity to the development of genotypic resistance. Time-lapse microscopy reveals that antibiotic-susceptible pneumococci display remarkable growth and death bistability patterns in response to many antibiotics. We furthermore capture the rise of subpopulations with decreased susceptibility towards cell wall synthesis inhibitors (heteroresisters). We show that this phenomenon is epigenetically inherited, and that heteroresistance potentiates the accumulation of genotypic resistance. The emergence of antibiotic resistance in bacteria is driven by inhibitory but non-lethal antibiotic concentrations. Here, Sorg and Veening study the effects of different antibiotics on the pneumococcus, with a focus on inhibition dynamics, metabolic activity and processes at the single-cell level.
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Differences in antibiotic-induced oxidative stress responses between laboratory and clinical isolates of Streptococcus pneumoniae. Antimicrob Agents Chemother 2015; 59:5420-6. [PMID: 26100702 DOI: 10.1128/aac.00316-15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 06/15/2015] [Indexed: 11/20/2022] Open
Abstract
Oxidants were shown to contribute to the lethality of bactericidal antibiotics in different bacterial species, including the laboratory strain Streptococcus pneumoniae R6. Resistance to penicillin among S. pneumoniae R6 mutants was further shown to protect against the induction of oxidants upon exposure to unrelated bactericidal compounds. In the work described here, we expanded on these results by studying the accumulation of reactive oxygen species in the context of antibiotic sensitivity and resistance by including S. pneumoniae clinical isolates. In S. pneumoniae R6, penicillin, ciprofloxacin, and kanamycin but not the bacteriostatic linezolid, erythromycin, or tetracycline induced the accumulation of reactive oxygen species. For the three bactericidal compounds, resistance to a single molecule prevented the accumulation of oxidants upon exposure to unrelated bactericidal antibiotics, and this was accompanied by a reduced lethality. This phenomenon does not involve target site mutations but most likely implicates additional mutations occurring early during the selection of resistance to increase survival while more efficient resistance mechanisms are being selected or acquired. Bactericidal antibiotics also induced oxidants in sensitive S. pneumoniae clinical isolates. The importance of oxidants in the lethality of bactericidal antibiotics was less clear than for S. pneumoniae R6, however, since ciprofloxacin induced oxidants even in ciprofloxacin-resistant S. pneumoniae clinical isolates. Our results provide a clear example of the complex nature of the mode of action of antibiotics. The adaptive approach to oxidative stress of S. pneumoniae is peculiar, and a better understanding of the mechanism implicated in response to oxidative injury should also help clarify the role of oxidants induced by antibiotics.
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Chaguza C, Cornick JE, Everett DB. Mechanisms and impact of genetic recombination in the evolution of Streptococcus pneumoniae. Comput Struct Biotechnol J 2015; 13:241-7. [PMID: 25904996 PMCID: PMC4404416 DOI: 10.1016/j.csbj.2015.03.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 03/27/2015] [Accepted: 03/31/2015] [Indexed: 02/04/2023] Open
Abstract
Streptococcus pneumoniae (the pneumococcus) is a highly recombinogenic bacterium responsible for a high burden of human disease globally. Genetic recombination, a process in which exogenous DNA is acquired and incorporated into its genome, is a key evolutionary mechanism employed by the pneumococcus to rapidly adapt to selective pressures. The rate at which the pneumococcus acquires genetic variation through recombination is much higher than the rate at which the organism acquires variation through spontaneous mutations. This higher rate of variation allows the pneumococcus to circumvent the host innate and adaptive immune responses, escape clinical interventions, including antibiotic therapy and vaccine introduction. The rapid influx of whole genome sequence (WGS) data and the advent of novel analysis methods and powerful computational tools for population genetics and evolution studies has transformed our understanding of how genetic recombination drives pneumococcal adaptation and evolution. Here we discuss how genetic recombination has impacted upon the evolution of the pneumococcus.
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Affiliation(s)
- Chrispin Chaguza
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, L69 7BE Liverpool, UK
| | - Jennifer E Cornick
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, L69 7BE Liverpool, UK
| | - Dean B Everett
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, L69 7BE Liverpool, UK
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Zhang J, Yang YH, Jiang YL, Zhou CZ, Chen Y. Structural and biochemical analyses of the Streptococcus pneumonia L,D-carboxypeptidase DacB. ACTA ACUST UNITED AC 2015; 71:283-92. [PMID: 25664738 DOI: 10.1107/s1399004714025371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 11/19/2014] [Indexed: 11/10/2022]
Abstract
The L,D-carboxypeptidase DacB plays a key role in the remodelling of Streptococcus pneumoniae peptidoglycan during cell division. In order to decipher its substrate-binding properties and catalytic mechanism, the 1.71 Å resolution crystal structure of DacB from S. pneumoniae TIGR4 is reported. Structural analyses in combination with comparisons with the recently reported structures of DacB from S. pneumoniae D39 and R6 clearly demonstrate that DacB adopts a zinc-dependent carboxypeptidase fold and belongs to the metallopeptidase M15B subfamily. In addition, enzymatic activity assays further confirm that DacB indeed acts as an L,D-carboxypeptidase towards the tetrapeptide L-Ala-D-iGln-L-Lys-D-Ala of the peptidoglycan stem, with Km and kcat values of 2.84 ± 0.37 mM and 91.49 ± 0.05 s(-1), respectively. Subsequent molecular docking and site-directed mutagenesis enable the assignment of the key residues that bind to the tetrapeptide. Altogether, these findings provide structural insights into substrate recognition in the metallopeptidase M15B subfamily.
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Affiliation(s)
- Juan Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, People's Republic of China
| | - Yi-Hu Yang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, People's Republic of China
| | - Yong-Liang Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, People's Republic of China
| | - Cong-Zhao Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, People's Republic of China
| | - Yuxing Chen
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, People's Republic of China
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Fair RJ, Tor Y. Antibiotics and bacterial resistance in the 21st century. PERSPECTIVES IN MEDICINAL CHEMISTRY 2014; 6:25-64. [PMID: 25232278 PMCID: PMC4159373 DOI: 10.4137/pmc.s14459] [Citation(s) in RCA: 866] [Impact Index Per Article: 86.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 06/24/2014] [Accepted: 06/24/2014] [Indexed: 12/11/2022]
Abstract
Dangerous, antibiotic resistant bacteria have been observed with increasing frequency over the past several decades. In this review the factors that have been linked to this phenomenon are addressed. Profiles of bacterial species that are deemed to be particularly concerning at the present time are illustrated. Factors including economic impact, intrinsic and acquired drug resistance, morbidity and mortality rates, and means of infection are taken into account. Synchronously with the waxing of bacterial resistance there has been waning antibiotic development. The approaches that scientists are employing in the pursuit of new antibacterial agents are briefly described. The standings of established antibiotic classes as well as potentially emerging classes are assessed with an emphasis on molecules that have been clinically approved or are in advanced stages of development. Historical perspectives, mechanisms of action and resistance, spectrum of activity, and preeminent members of each class are discussed.
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Affiliation(s)
- Richard J Fair
- Department for Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Berlin, Germany
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
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Meiers M, Volz C, Eisel J, Maurer P, Henrich B, Hakenbeck R. Altered lipid composition in Streptococcus pneumoniae cpoA mutants. BMC Microbiol 2014; 14:12. [PMID: 24443834 PMCID: PMC3901891 DOI: 10.1186/1471-2180-14-12] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 01/16/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Penicillin-resistance in Streptococcus pneumoniae is mainly due to alterations in genes encoding the target enzymes for beta-lactams, the penicillin-binding proteins (PBPs). However, non-PBP genes are altered in beta-lactam-resistant laboratory mutants and confer decreased susceptibility to beta-lactam antibiotics. Two piperacillin resistant laboratory mutants of Streptococcus pneumoniae R6 contain mutations in the putative glycosyltransferase gene cpoA. The CpoA gene is part of an operon including another putative glycosyltransferase gene spr0982, both of which being homologous to glycolipid synthases present in other Gram-positive bacteria. RESULTS We now show that the cpoA mutants as well as a cpoA deletion mutant are defective in the synthesis of galactosyl-glucosyl-diacylglycerol (GalGlcDAG) in vivo consistent with the in vitro function of CpoA as α-GalGlcDAG synthase as shown previously. In addition, the proportion of phosphatidylglycerol increased relative to cardiolipin in cpoA mutants. Moreover, cpoA mutants are more susceptible to acidic stress, have an increased requirement for Mg(2+) at low pH, reveal a higher resistance to lysis inducing conditions and are hypersensitive to bacitracin. CONCLUSIONS The data show that deficiency of the major glycolipid GalGlcDAG causes a pleitotropic phenotype of cpoA mutant cells consistent with severe membrane alterations. We suggest that the cpoA mutations selected with piperacillin are directed against the lytic response induced by the beta-lactam antibiotic.
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Affiliation(s)
| | | | | | | | | | - Regine Hakenbeck
- Department of Microbiology, University of Kaiserslautern, Gottlieb-Daimler-Strasse, Gebäude 23, D-67663 Kaiserslautern, Germany.
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Genomic analyses of DNA transformation and penicillin resistance in Streptococcus pneumoniae clinical isolates. Antimicrob Agents Chemother 2013; 58:1397-403. [PMID: 24342643 DOI: 10.1128/aac.01311-13] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Alterations in penicillin-binding proteins, the target enzymes for β-lactam antibiotics, are recognized as primary penicillin resistance mechanisms in Streptococcus pneumoniae. Few studies have analyzed penicillin resistance at the genome scale, however, and we report the sequencing of S. pneumoniae R6 transformants generated while reconstructing the penicillin resistance phenotypes from three penicillin-resistant clinical isolates by serial genome transformation. The genome sequences of the three last-level transformants T2-18209, T5-1983, and T3-55938 revealed that 16.2 kb, 82.7 kb, and 137.2 kb of their genomes had been replaced with 5, 20, and 37 recombinant sequence segments derived from their respective parental clinical isolates, documenting the extent of DNA transformation between strains. A role in penicillin resistance was confirmed for some of the mutations identified in the transformants. Several multiple recombination events were also found to have happened at single loci coding for penicillin-binding proteins (PBPs) that increase resistance. Sequencing of the transformants with MICs for penicillin similar to those of the parent clinical strains confirmed the importance of mosaic PBP2x, -2b, and -1a as a driving force in penicillin resistance. A role in resistance for mosaic PBP2a was also observed for two of the resistant clinical isolates.
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McDougall S, Hussein H, Petrovski K. Antimicrobial resistance in Staphylococcus aureus, Streptococcus uberis and Streptococcus dysgalactiae from dairy cows with mastitis. N Z Vet J 2013; 62:68-76. [PMID: 24215609 DOI: 10.1080/00480169.2013.843135] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
AIMS To determine the minimal inhibitory concentrations (MIC) of antimicrobials for common mastitis pathogens from dairy cows in New Zealand; and to assess the effect of source of the isolates, i.e. commercial veterinary laboratories or collected as part of research studies; the clinical status of the cow, i.e. subclinical or clinical mastitis; cow age and herd on the distribution of the MIC. METHODS Minimal inhibitory concentrations for Staphylococcus aureus (n=364), Streptococcus dysgalactiae (n=65) and Streptococcus uberis (n=102) isolated from milk samples from dairy cows were determined for a variety of antimicrobials using broth microdilution. Isolates of S. aureus were sourced from research studies from both subclinically (n=161) and clinically (n=104) affected cows, as well as from commercial veterinary laboratories (n=101); while all the streptococcal isolates were from commercial laboratories. Resistance was defined using the cut-points provided by the Clinical and Laboratory Standards Institute (CLSI). RESULTS The distribution of MIC varied among the bacterial species for every antimicrobial tested (p<0.001). Of the S. aureus isolates, 28, 2 and 0.5% were resistant to penicillin, ampicillin and trimethoprim/sulfamethoxazole, respectively. For S. dysgalactiae and S. uberis isolates, 17 and 13% were resistant to trimethoprim/sulfamethoxazole, respectively. One isolate (1%) of S. uberis was resistant to penicillin. The distribution of MIC of S. aureus varied with clinical status, between herds, and with age of cow (p<0.05). The distribution of MIC for S. aureus for penicillin, amoxicillin/clavulanic acid, cloxacillin and ampicillin were lower from clinical than subclinical cases, and those for amoxicillin/clavulanic acid and oxytetracycline from isolates from veterinary laboratories were lower than for those from research studies. CONCLUSIONS Resistance to some beta-lactam antimicrobials and trimethoprim/sulfamethoxazole were found in isolates from cases of bovine mastitis. The distribution of MIC for isolates of S. aureus varied with clinical status of the cow, the age of the cow, the herd and with the source of isolate. CLINICAL SIGNIFICANCE Resistance to penicillin was found in a quarter of S. aureus isolates, but in virtually no Streptococcus isolates; therefore microbial identification and sensitivity testing would be beneficial when assessing treatment options. The source of the isolates affected the estimated MIC, suggesting that selection of isolates for monitoring of resistance requires care and that use of routine submissions to commercial laboratories to assess antimicrobial resistance patterns may result in biased estimates of prevalence of resistance.
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Affiliation(s)
- S McDougall
- a Cognosco, Anexa Animal Health , PO Box 21, Morrinsville , New Zealand
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Frazão N, Hiller NL, Powell E, Earl J, Ahmed A, Sá-Leão R, de Lencastre H, Ehrlich GD, Tomasz A. Virulence potential and genome-wide characterization of drug resistant Streptococcus pneumoniae clones selected in vivo by the 7-valent pneumococcal conjugate vaccine. PLoS One 2013; 8:e74867. [PMID: 24069360 PMCID: PMC3777985 DOI: 10.1371/journal.pone.0074867] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 08/07/2013] [Indexed: 11/28/2022] Open
Abstract
We used mouse models of pneumococcal colonization and disease combined with full genome sequencing to characterize three major drug resistant clones of S. pneumoniae that were recovered from the nasopharynx of PCV7-immunized children in Portugal. The three clones--serotype 6A (ST2191), serotype 15A (ST63) and serotype 19A (ST276) carried some of the same drug resistance determinants already identified in nasopharyngeal isolates from the pre-PCV7 era. The three clones were able to colonize efficiently the mouse nasopharyngeal mucosa where populations of these pneumococci were retained for as long as 21 days. During this period, the three clones were able to asymptomatically invade the olfactory bulbs, brain, lungs and the middle ear mucosa and established populations in these tissues. The virulence potential of the three clones was poor even at high inoculum (10(5) CFU per mouse) concentrations in the mouse septicemia model and was undetectable in the pneumonia model. Capsular type 3 transformants of clones 6A and 19A prepared in the laboratory produced lethal infection at low cell concentration (10(3) CFU per mouse) but the same transformants became impaired in their potential to colonize, indicating the importance of the capsular polysaccharide in both disease and colonization. The three clones were compared to the genomes of 56 S. pneumoniae strains for which sequence information was available in the public databank. Clone 15A (ST63) only differed from the serotype 19F clone G54 in a very few genes including serotype so that this clone may be considered the product of a capsular switch. While no strain with comparable degree of similarity to clone 19A (ST276) was found among the sequenced isolates, by MLST this clone is a single locust variant (SLV) of Denmark14-ST230 international clone. Clone 6A (ST2191) was most similar to the penicillin resistant Hungarian serotype 19A clone.
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Affiliation(s)
- Nelson Frazão
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
- Laboratory of Microbiology, The Rockefeller University, New York, New York, United States of America
| | - N. Luisa Hiller
- Allegheny General Hospital, Allegheny-Singer Research Institute, Center for Genomic Sciences, Pittsburgh, Pennsylvania, United States of America
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Evan Powell
- Allegheny General Hospital, Allegheny-Singer Research Institute, Center for Genomic Sciences, Pittsburgh, Pennsylvania, United States of America
| | - Josh Earl
- Allegheny General Hospital, Allegheny-Singer Research Institute, Center for Genomic Sciences, Pittsburgh, Pennsylvania, United States of America
| | - Azad Ahmed
- Allegheny General Hospital, Allegheny-Singer Research Institute, Center for Genomic Sciences, Pittsburgh, Pennsylvania, United States of America
| | - Raquel Sá-Leão
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Hermínia de Lencastre
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
- Laboratory of Microbiology, The Rockefeller University, New York, New York, United States of America
| | - Garth D. Ehrlich
- Allegheny General Hospital, Allegheny-Singer Research Institute, Center for Genomic Sciences, Pittsburgh, Pennsylvania, United States of America
| | - Alexander Tomasz
- Laboratory of Microbiology, The Rockefeller University, New York, New York, United States of America
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Reverón I, Rodríguez H, Campos G, Curiel JA, Ascaso C, Carrascosa AV, Prieto A, de las Rivas B, Muñoz R, de Felipe FL. Tannic acid-dependent modulation of selected Lactobacillus plantarum traits linked to gastrointestinal survival. PLoS One 2013; 8:e66473. [PMID: 23776675 PMCID: PMC3679024 DOI: 10.1371/journal.pone.0066473] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 05/08/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Owing to its antimicrobial properties dietary tannins may alter the functional efficacy of probiotic lactobacilli in the gastrointestinal (GI)-tract influencing their growth, viability and molecular adaptation to the intestinal environment. METHODS AND FINDINGS The effects of tannic acid on Lactobacillus plantarum WCFS1 were studied by in vitro growth monitoring and visualizing the morphological alteration on the cell wall using transmission electron microscopy. Growth upon tannic acid was characterized by dose-dependent reductions of initial viable counts and extended lag phases. Lag phase-cells growing upon 0.5 mM tannic acid were abnormally shaped and experienced disturbance on the cell wall such as roughness, occasional leakage and release of cell debris, but resumed growth later at tannic acid concentrations high as 2.5 mM. To gain insight on how the response to tannic acid influenced the molecular adaptation of L. plantarum to the GI-tract conditions, gene expression of selected biomarkers for GI-survival was assessed by RT-qPCR on cDNA templates synthetized from mRNA samples obtained from cells treated with 0.5 or 2 mM tannic acid. Tannic acid-dependent gene induction was confirmed for selected genes highly expressed in the gut or with confirmed roles in GI-survival. No differential expression was observed for the pbp2A gene, a biomarker negatively related with GI-survival. However PBP2A was not labeled by Bocillin FL, a fluorescent dye-labeled penicillin V derivative, in the presence of tannic acid which suggests for enhanced GI-survival reportedly associated with the inactivation of this function. CONCLUSIONS Probiotic L. plantarum WCFS1 is able to overcome the toxic effects of tannic acid. This dietary constituent modulates molecular traits linked to the adaptation to intestinal environment in ways previously shown to enhance GI-survival.
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Affiliation(s)
- Inés Reverón
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de los Alimentos y Nutrición, Consejo Superior de Investigaciones Científicas (ICTAN-CSIC), Madrid, Spain
| | - Héctor Rodríguez
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de los Alimentos y Nutrición, Consejo Superior de Investigaciones Científicas (ICTAN-CSIC), Madrid, Spain
| | - Gema Campos
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de los Alimentos y Nutrición, Consejo Superior de Investigaciones Científicas (ICTAN-CSIC), Madrid, Spain
| | - José Antonio Curiel
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de los Alimentos y Nutrición, Consejo Superior de Investigaciones Científicas (ICTAN-CSIC), Madrid, Spain
| | - Carmen Ascaso
- Dpto. Biología Ambiental, Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas (MNCN-CSIC), Madrid, Spain
| | - Alfonso V. Carrascosa
- Grupo de Microbiología y Biocatálisis de Alimentos, Instituto de Investigación en Ciencias de la Alimentación, Consejo Superior de Investigaciones Científicas (CIAL-CSIC), Madrid, Spain
| | - Alicia Prieto
- Dpto. Biología Medioambiental, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CIB-CSIC), Madrid, Spain
| | - Blanca de las Rivas
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de los Alimentos y Nutrición, Consejo Superior de Investigaciones Científicas (ICTAN-CSIC), Madrid, Spain
| | - Rosario Muñoz
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de los Alimentos y Nutrición, Consejo Superior de Investigaciones Científicas (ICTAN-CSIC), Madrid, Spain
| | - Félix López de Felipe
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de los Alimentos y Nutrición, Consejo Superior de Investigaciones Científicas (ICTAN-CSIC), Madrid, Spain
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Fani F, Brotherton MC, Leprohon P, Ouellette M. Genomic analysis and reconstruction of cefotaxime resistance in Streptococcus pneumoniae. J Antimicrob Chemother 2013; 68:1718-27. [PMID: 23608923 DOI: 10.1093/jac/dkt113] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES To identify non-penicillin-binding protein (PBP) mutations contributing to resistance to the third-generation cephalosporin cefotaxime in Streptococcus pneumoniae at the genome-wide scale. METHODS The genomes of two in vitro S. pneumoniae cefotaxime-resistant isolates and of two transformants serially transformed with the genomic DNA of cefotaxime-resistant mutants were determined by next-generation sequencing. A role in cefotaxime resistance for the mutations identified was confirmed by reconstructing resistance in a cefotaxime-susceptible background. RESULTS Analysis of the genome assemblies revealed mutations in genes coding for the PBPs 2x, 2a and 3, of which pbp2x was the only mutated gene common to all mutants. The transformation of altered PBP alleles into S. pneumoniae R6 confirmed the role of PBP mutations in cefotaxime resistance, but these were not sufficient to fully explain the levels of resistance. Thirty-one additional genes were found to be mutated in at least one of the four sequenced genomes. Non-PBP resistance determinants appeared to be mostly lineage specific. Mutations in spr1333, spr0981, spr1704 and spr1098, encoding a peptidoglycan N-acetylglucosamine deacetylase, a glycosyltransferase, an ABC transporter and a sortase, respectively, were implicated in resistance by transformation experiments and allowed the reconstruction of the full level of resistance observed in the parent resistant strains. CONCLUSIONS This whole-genome analysis coupled to functional studies has allowed the discovery of both known and novel cefotaxime resistance genes in S. pneumoniae.
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Affiliation(s)
- Fereshteh Fani
- Centre de recherche en Infectiologie du Centre de recherche du CHUL and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, Canada
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Heteroresistance to fosfomycin is predominant in Streptococcus pneumoniae and depends on the murA1 gene. Antimicrob Agents Chemother 2013; 57:2801-8. [PMID: 23571543 DOI: 10.1128/aac.00223-13] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fosfomycin targets the first step of peptidoglycan biosynthesis in Streptococcus pneumoniae catalyzed by UDP-N-acetylglucosamine enolpyruvyltransferase (MurA1). We investigated whether heteroresistance to fosfomycin occurs in S. pneumoniae. We found that of 11 strains tested, all but 1 (Hungary(19A)) displayed heteroresistance and that deletion of murA1 abolished heteroresistance. Hungary(19A) differs from the other strains by a single amino acid substitution in MurA1 (Ala(364)Thr). To test whether this substitution is responsible for the lack of heteroresistance, it was introduced into strain D39. The heteroresistance phenotype of strain D39 was not changed. Furthermore, no relevant structural differences between the MurA1 crystal structures of heteroresistant strain D39 and nonheteroresistant strain Hungary(19A) were found. Our results reveal that heteroresistance to fosfomycin is the predominant phenotype of S. pneumoniae and that MurA1 is required for heteroresistance to fosfomycin but is not the only factor involved. The findings provide a caveat for any future use of fosfomycin in the treatment of pneumococcal infections.
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Wyres KL, Lambertsen LM, Croucher NJ, McGee L, von Gottberg A, Liñares J, Jacobs MR, Kristinsson KG, Beall BW, Klugman KP, Parkhill J, Hakenbeck R, Bentley SD, Brueggemann AB. The multidrug-resistant PMEN1 pneumococcus is a paradigm for genetic success. Genome Biol 2012; 13:R103. [PMID: 23158461 PMCID: PMC3580495 DOI: 10.1186/gb-2012-13-11-r103] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 10/16/2012] [Accepted: 11/16/2012] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Streptococcus pneumoniae, also called the pneumococcus, is a major bacterial pathogen. Since its introduction in the 1940s, penicillin has been the primary treatment for pneumococcal diseases. Penicillin resistance rapidly increased among pneumococci over the past 30 years, and one particular multidrug-resistant clone, PMEN1, became highly prevalent globally. We studied a collection of 426 pneumococci isolated between 1937 and 2007 to better understand the evolution of penicillin resistance within this species. RESULTS We discovered that one of the earliest known penicillin-nonsusceptible pneumococci, recovered in 1967 from Australia, was the likely ancestor of PMEN1, since approximately 95% of coding sequences identified within its genome were highly similar to those of PMEN1. The regions of the PMEN1 genome that differed from the ancestor contained genes associated with antibiotic resistance, transmission and virulence. We also revealed that PMEN1 was uniquely promiscuous with its DNA, donating penicillin-resistance genes and sometimes many other genes associated with antibiotic resistance, virulence and cell adherence to many genotypically diverse pneumococci. In particular, we describe two strains in which up to 10% of the PMEN1 genome was acquired in multiple fragments, some as long as 32 kb, distributed around the recipient genomes. This type of directional genetic promiscuity from a single clone to numerous unrelated clones has, to our knowledge, never before been described. CONCLUSIONS These findings suggest that PMEN1 is a paradigm of genetic success both through its epidemiology and promiscuity. These findings also challenge the existing views about horizontal gene transfer among pneumococci.
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Affiliation(s)
- Kelly L Wyres
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Lotte M Lambertsen
- Department of Microbiology Surveillance and Research, Statens Serum Institut, 5 Artillerivej, DK 2300 Copenhagen S, Denmark
| | - Nicholas J Croucher
- Pathogen Genomics Team, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Lesley McGee
- Streptococcus Laboratory, Centers for Disease Control and Prevention, 1600 Clifton Rd, Atlanta, Georgia, 30333, USA
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Sandringham, Johannesburg 2131, South Africa
| | - Josefina Liñares
- Department of Microbiology, Bellvitge Hospital-CIBERes-IDIBELL-UB, Feixa Llarga s/n, 08907 Barcelona, Spain
| | - Michael R Jacobs
- Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Karl G Kristinsson
- Clinical Microbiology Department, Landspitali University Hospital and University of Iceland, 101 Reykjavik, Iceland
| | - Bernard W Beall
- Streptococcus Laboratory, Centers for Disease Control and Prevention, 1600 Clifton Rd, Atlanta, Georgia, 30333, USA
| | - Keith P Klugman
- Hubert Department of Global Health Epidemiology, Rollins School of Public Health, 1518 Clifton Road NE, Atlanta, GA 30322, USA
| | - Julian Parkhill
- Pathogen Genomics Team, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Regine Hakenbeck
- Department of Microbiology, University Kaiserslautern, Paul-Ehrlich-Straße, 67663 Kaiserslautern, Germany
| | - Stephen D Bentley
- Pathogen Genomics Team, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Angela B Brueggemann
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
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Hakenbeck R, Brückner R, Denapaite D, Maurer P. Molecular mechanisms of β-lactam resistance in Streptococcus pneumoniae. Future Microbiol 2012; 7:395-410. [PMID: 22393892 DOI: 10.2217/fmb.12.2] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Alterations in the target enzymes for β-lactam antibiotics, the penicillin-binding proteins (PBPs), have been recognized as a major resistance mechanism in Streptococcus pneumoniae. Mutations in PBPs that confer a reduced affinity to β-lactams have been identified in laboratory mutants and clinical isolates, and document an astounding variability of sites involved in this phenotype. Whereas point mutations are selected in the laboratory, clinical isolates display a mosaic structure of the affected PBP genes, the result of interspecies gene transfer and recombination events. Depending on the selective β-lactam, different combinations of PBP genes and mutations within are involved in conferring resistance, and astoundingly in non-PBP genes as well.
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Affiliation(s)
- Regine Hakenbeck
- Department of Microbiology, University of Kaiserslautern, Paul Ehrlich Strasse 23, D-67663 Kaiserslautern, Germany.
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Krueger B, Friedrich T, Förster F, Bernhardt J, Gross R, Dandekar T. Different evolutionary modifications as a guide to rewire two-component systems. Bioinform Biol Insights 2012; 6:97-128. [PMID: 22586357 PMCID: PMC3348925 DOI: 10.4137/bbi.s9356] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Two-component systems (TCS) are short signalling pathways generally occurring in prokaryotes. They frequently regulate prokaryotic stimulus responses and thus are also of interest for engineering in biotechnology and synthetic biology. The aim of this study is to better understand and describe rewiring of TCS while investigating different evolutionary scenarios. Based on large-scale screens of TCS in different organisms, this study gives detailed data, concrete alignments, and structure analysis on three general modification scenarios, where TCS were rewired for new responses and functions: (i) exchanges in the sequence within single TCS domains, (ii) exchange of whole TCS domains; (iii) addition of new components modulating TCS function. As a result, the replacement of stimulus and promotor cassettes to rewire TCS is well defined exploiting the alignments given here. The diverged TCS examples are non-trivial and the design is challenging. Designed connector proteins may also be useful to modify TCS in selected cases.
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Affiliation(s)
- Beate Krueger
- Dept of Bioinformatics, Biocenter, Am Hubland, University of Würzburg, D-97074 Würzburg, Germany
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Fani F, Leprohon P, Légaré D, Ouellette M. Whole genome sequencing of penicillin-resistant Streptococcus pneumoniae reveals mutations in penicillin-binding proteins and in a putative iron permease. Genome Biol 2011; 12:R115. [PMID: 22108223 PMCID: PMC3334601 DOI: 10.1186/gb-2011-12-11-r115] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2011] [Revised: 09/29/2011] [Accepted: 11/22/2011] [Indexed: 01/10/2023] Open
Affiliation(s)
- Fereshteh Fani
- Centre de recherche en Infectiologie du Centre de recherche du CHUL and Département de Microbiologie, Infectiologie et Immunologie, Université Laval, Laurier, Québec, Canada
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Novel mutations in a patient isolate of Streptococcus agalactiae with reduced penicillin susceptibility emerging after long-term oral suppressive therapy. Antimicrob Agents Chemother 2011; 55:2983-5. [PMID: 21383092 DOI: 10.1128/aac.01243-10] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Penicillin nonsusceptibility has been demonstrated in group B streptococci (GBS), but there is limited information regarding mechanisms of resistance. We report a case of GBS with reduced susceptibility to penicillin emerging after long-term suppressive oral penicillin therapy for a prosthetic joint infection. Molecular characterization of the isolate before and after long-term penicillin therapy revealed 5 mutations in the ligand-binding regions of PBP1a, -2a, and -2x not previously reported in GBS.
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41
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Analysis of cytoplasmic membrane proteome of Streptococcus pneumoniae by shotgun proteomic approach. J Microbiol 2011; 48:872-6. [DOI: 10.1007/s12275-010-0220-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Accepted: 09/08/2010] [Indexed: 11/26/2022]
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Penicillin-binding protein gene alterations in Streptococcus uberis isolates presenting decreased susceptibility to penicillin. Antimicrob Agents Chemother 2010; 54:1140-5. [PMID: 20065061 DOI: 10.1128/aac.00915-09] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Streptococcus uberis is an environmental pathogen commonly causing bovine mastitis, an infection that is generally treated with penicillin G. No field case of true penicillin-resistant S. uberis (MIC > 16 mg/liter) has been described yet, but isolates presenting decreased susceptibility (MIC of 0.25 to 0.5 mg/liter) to this drug are regularly reported to our laboratory. In this study, we demonstrated that S. uberis can readily develop penicillin resistance in laboratory-evolved mutants. The molecular mechanism of resistance (acquisition of mutations in penicillin-binding protein 1A [PBP1A], PBP2B, and PBP2X) was generally similar to that of all other penicillin-resistant streptococci described so far. In addition, it was also specific to S. uberis in that independent resistant mutants carried a unique set of seven consensus mutations, of which only one (Q(554)E in PBP2X) was commonly found in other streptococci. In parallel, independent isolates from bovine mastitis with different geographical origins (France, Holland, and Switzerland) and presenting a decreased susceptibility to penicillin were characterized. No mosaic PBPs were detected, but they all presented mutations identical to the one found in the laboratory-evolved mutants. This indicates that penicillin resistance development in S. uberis might follow a stringent pathway that would explain, in addition to the ecological niche of this pathogen, why naturally occurring resistances are still rare. In addition, this study shows that there is a reservoir of mutated PBPs in animals, which might be exchanged with other streptococci, such as Streptococcus agalactiae, that could potentially be transmitted to humans.
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Dias R, Félix D, Caniça M, Trombe MC. The highly conserved serine threonine kinase StkP of Streptococcus pneumoniae contributes to penicillin susceptibility independently from genes encoding penicillin-binding proteins. BMC Microbiol 2009; 9:121. [PMID: 19500353 PMCID: PMC2700816 DOI: 10.1186/1471-2180-9-121] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2008] [Accepted: 06/05/2009] [Indexed: 11/12/2022] Open
Abstract
Background The serine/threonine kinase StkP of Streptococcus pneumoniae is a major virulence factor in the mouse model of infection. StkP is a modular protein with a N-terminal kinase domain a C-terminal PASTA domain carrying the signature of penicillin-binding protein (PBP) and prokaryotic serine threonine kinase. In laboratory cultures, one target of StkP is the phosphoglucosamine mutase GlmM involved in the first steps of peptidoglycan biosynthesis. In order to further elucidate the importance of StkP in S. pneumoniae, its role in resistance to β-lactams has been assessed by mutational analysis in laboratory cultures and its genetic conservation has been investigated in isolates from infected sites (virulent), asymptomatic carriers, susceptible and non-susceptible to β-lactams. Results Deletion replacement mutation in stkP conferred hypersensitivity to penicillin G and was epistatic on mutations in PBP2X, PBP2B and PBP1A from the resistant 9V clinical isolate URA1258. Genetic analysis of 55 clinical isolates identified 11 StkP alleles differing from the reference R6 allele. None relevant mutation in the kinase or the PASTA domains were found to account for susceptibility of the isolates. Rather the minimal inhibitory concentration (MIC) values of the strains appeared to be determined by their PBP alleles. Conclusion The results of genetic dissection analysis in lab strain Cp1015 reveal that StkP is involved in the bacterial response to penicillin and is epistatic on mutations PBP 2B, 2X and 1A. However analysis of the clinical isolates did not allow us to find the StkP alleles putatively involved in determining the virulence or the resistance level of a given strain, suggesting a strong conservation of StkP in clinical isolates.
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Affiliation(s)
- Ricardo Dias
- Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal.
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Johnsborg O, Håvarstein LS. Regulation of natural genetic transformation and acquisition of transforming DNA in Streptococcus pneumoniae. FEMS Microbiol Rev 2009; 33:627-42. [PMID: 19396959 DOI: 10.1111/j.1574-6976.2009.00167.x] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The ability of pneumococci to take up naked DNA from the environment and permanently incorporate the DNA into their genome by recombination has been exploited as a valuable research tool for 80 years. From being viewed as a marginal phenomenon, it has become increasingly clear that horizontal gene transfer by natural transformation is a powerful mechanism for generating genetic diversity, and that it has the potential to cause severe problems for future treatment of pneumococcal disease. This process constitutes a highly efficient mechanism for spreading beta-lactam resistance determinants between streptococcal strains and species, and also threatens to undermine the effect of pneumococcal vaccines. Fortunately, great progress has been made during recent decades to elucidate the mechanism behind natural transformation at a molecular level. Increased insight into these matters will be important for future development of therapeutic strategies and countermeasures aimed at reducing the spread of hazardous traits. In this review, we focus on recent developments in our understanding of competence regulation, DNA acquisition and the role of natural transformation in the dissemination of virulence and beta-lactam resistance determinants.
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Affiliation(s)
- Ola Johnsborg
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, As, Norway
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Abstract
Horizontal gene transfer (HGT) has been responsible for the dissemination of numerous antimicrobial-resistance determinants throughout diverse bacterial species. The rapid and broad dissemination of resistance determinants by HGT, and subsequent selection for resistance imposed by the use of antimicrobials, threatens to undermine the usefulness of antimicrobials. However, vigilant surveillance of the emerging antimicrobial resistance in clinical settings and subsequent studies of resistant isolates create a powerful system for studying HGT and detecting rare events. Two of the most closely monitored phenotypes are resistance to beta-lactams and resistance to fluoroquinolones. Studies of resistance to these antimicrobials have revealed that (1) transformation occurs between different species of bacteria including some recipient species that were not previously known to be competent for natural transformation; (2) transduction may be playing an important role in generating novel methicillin-resistant Staphylococcus aureus (MRSA) strains, although the details of transferring the SCCmec element are not yet fully understood; (3) Resistance genes are probably moving to plasmids from chromosomes more rapidly than in the past; and (4) Resistance genes are aggregating upon plasmids. The linkage of numerous resistance genes on individual plasmids may underlie the persistence of resistance to specific antimicrobials even when use of those antimicrobials is discontinued. Further studies of HGT and methods for controlling HGT may be necessary to maintain the usefulness of antimicrobials.
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46
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An important site in PBP2x of penicillin-resistant clinical isolates of Streptococcus pneumoniae: mutational analysis of Thr338. Antimicrob Agents Chemother 2008; 53:1107-15. [PMID: 19075056 DOI: 10.1128/aac.01107-08] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Penicillin-binding protein 2x (PBP2x) of Streptococcus pneumoniae represents a primary resistance determinant for beta-lactams, and low-affinity PBP2x variants can easily be selected with cefotaxime. Penicillin-resistant clinical isolates of S. pneumoniae frequently contain in their mosaic PBP2x the mutation T338A adjacent to the active site S337, and T338P as well as T338G substitutions are also known. Site-directed mutagenesis has now documented that a single point mutation at position T338 confers selectable levels of beta-lactam resistance preferentially to oxacillin. Despite the moderate impact on beta-lactam susceptibility, the function of the PBP2x mutants appears to be impaired, as can be documented in the absence of a functional CiaRH regulatory system, resulting in growth defects and morphological changes. The combination of low-affinity PBP2x and PBP1a encoded by mosaic genes is known to result in high cefotaxime resistance. In contrast, introduction of a mosaic pbp1a into the PBP2x(T338G) mutant did not lead to increased resistance. However, the mosaic PBP1a gene apparently complemented the PBP2x(T338G) defect, since Cia mutant derivatives grew normally. The data support the view that PBP2x and PBP1a interact with each other on some level and that alterations of both PBPs in resistant clinical isolates have evolved to ensure cooperation between both proteins.
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Recovery of susceptibility to penicillin G in clinical isolates of Streptococcus pneumoniae despite increased accumulation of pbp gene alterations. Int J Antimicrob Agents 2008; 32:427-31. [DOI: 10.1016/j.ijantimicag.2008.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2008] [Revised: 04/30/2008] [Accepted: 05/06/2008] [Indexed: 11/17/2022]
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Watanabe K, Anh DD, Huong PLT, Nguyet NT, Anh NTH, Thi NT, Dung NT, Phuong DM, Rusizoka OS, Nagatake T, Watanabe H, Oishi K. Drug-resistant pneumococci in children with acute lower respiratory infections in Vietnam. Pediatr Int 2008; 50:514-8. [PMID: 19143975 DOI: 10.1111/j.1442-200x.2008.02616.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND Acute lower respiratory infections (ALRI), primarily pneumonia, are the leading cause of death in children under 5 years of age. Most of these deaths occur in Africa and southeast Asia. Increasing rates of drug resistance in pneumococcal strains emphasize the necessity of prevention of pneumococcal vaccines. The aim of the present study was to determine the frequency of drug resistance and the distribution of serotype of pneumococcal strains isolated from pediatric patients with ALRI in Vietnam. METHODS Two hundred and twenty pediatric patients with ALRI under 5 years of age were enrolled in Hanoi, Vietnam between 2001 and 2002. Bacterial pathogens with a heavy growth (10(6) c.f.u./mL) were isolated from nasopharyngeal secretions on quantitative culture. Fifty-three pneumococcal strains isolated from the nasopharynx of pediatric patients were examined for antibiotic susceptibility including drug-resistant genes and serotyping. RESULTS A total of 73.6% of pneumococcal strains were genotypic penicillin-resistant Streptococcus pnemoniae (gPRSP), possessing altered penicillin-binding protein genes pbp 1a + 2x + 2b; 67.9% of these strains were gPRSP and simultaneously had the ermB gene, which is responsible for high resistance to erythromycin. The majority of gPRSP strains were serotype 19F or 23F. CONCLUSION gPRSP strains with serotype 19F or 23F are highly prevalent among pediatric patients with ALRI under 5 years of age in Hanoi, Vietnam.
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Affiliation(s)
- Kiwao Watanabe
- Department of Internal Medicine, International Research Center for Infectious Diseases, Institute of Microbial Diseases, Osaka University, Japan
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Opatowski L, Temime L, Varon E, Leclercq R, Leclerc R, Drugeon H, Boëlle PY, Guillemot D. Antibiotic innovation may contribute to slowing the dissemination of multiresistant Streptococcus pneumoniae: the example of ketolides. PLoS One 2008; 3:e2089. [PMID: 18461139 PMCID: PMC2330086 DOI: 10.1371/journal.pone.0002089] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2007] [Accepted: 03/24/2008] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Despite increasingly frequent bacterial resistance to antibiotics, antibacterial innovation is rare. Ketolides constitute one of the very few new antibiotic classes active against Streptococcus pneumoniae developed during the last 25 years. Their mechanism of action resembles that of macrolides, but they are unaffected by common resistance mechanisms. However, cross-resistance to ketolides has been observed in some macrolide-resistant strains. We examined how new antibiotic exposure may affect overall pneumococcal resistance patterns in the population. The aims of this study were to assess the potential dissemination of newly emerged resistances and to control the selection of strains already multiresistant to existing antimicrobials. METHODOLOGY/PRINCIPAL FINDINGS We developed an age-structured population model for S. pneumoniae transmission in a human community exposed to heptavalent vaccine, and beta-lactams, macrolides and ketolides. The dynamics of intra-individual selection of resistant strains under antibiotic exposure and interindividual transmission were simulated, with antibiotic-specific resistance mechanisms defining the path to co-resistances and cross-resistances, and parameters concerning the French situation. Results of this simulation study suggest that new antibiotic consumption could markedly slow the diffusion of multiresistant strains. Wider use was associated with slower progression of multiresistance. When ketolides were prescribed to all ages, resistance to them reached 10% after >15 years, while it took >40 years when they were prescribed only to adults. In the scenario according to which new antibiotics totally replaced former antimicrobials, the beta-lactam resistance rate was limited at 70%. CONCLUSIONS In a context of widespread vaccination and rational use of antibiotics, innovative antibiotic, prescribed to all age groups, may have an added impact on multiresistant-strain dissemination in the population.
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Affiliation(s)
- Lulla Opatowski
- Unité de Pharmacoépidémiologie et Maladies Infectieuses, Institut Pasteur, Paris, France.
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Rapid identification of penicillin and macrolide resistance genes and simultaneous quantification of Streptococcus pneumoniae in purulent sputum samples by use of a novel real-time multiplex PCR assay. J Clin Microbiol 2008; 46:2384-8. [PMID: 18463207 DOI: 10.1128/jcm.00051-08] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We evaluated a real-time quantitative PCR combined with a multiplex PCR assay for the quantification of Streptococcus pneumoniae and the simultaneous detection of drug-resistant genes by gel-based PCR, using purulent sputum samples. This assay correctly quantified S. pneumoniae and identified their penicillin and erythromycin susceptibilities directly from samples within 3 h.
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