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Kekeisen-Chen JF, Tarbangdo FT, Sharma S, Marasini D, Marjuki H, Kibler JL, Reese HE, Ouattara S, Ake FH, Yameogo I, Ouedraogo I, Seini E, Zoma RL, Tonde I, Sanou M, Novak RT, McNamara LA. Expansion of Neisseria meningitidis Serogroup C Clonal Complex 10217 during Meningitis Outbreak, Burkina Faso, 2019. Emerg Infect Dis 2024; 30:460-468. [PMID: 38407254 PMCID: PMC10902552 DOI: 10.3201/eid3003.221760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024] Open
Abstract
During January 28-May 5, 2019, a meningitis outbreak caused by Neisseria meningitidis serogroup C (NmC) occurred in Burkina Faso. Demographic and laboratory data for meningitis cases were collected through national case-based surveillance. Cerebrospinal fluid was collected and tested by culture and real-time PCR. Among 301 suspected cases reported in 6 districts, N. meningitidis was the primary pathogen detected; 103 cases were serogroup C and 13 were serogroup X. Whole-genome sequencing revealed that 18 cerebrospinal fluid specimens tested positive for NmC sequence type (ST) 10217 within clonal complex 10217, an ST responsible for large epidemics in Niger and Nigeria. Expansion of NmC ST10217 into Burkina Faso, continued NmC outbreaks in the meningitis belt of Africa since 2019, and ongoing circulation of N. meningitidis serogroup X in the region underscore the urgent need to use multivalent conjugate vaccines in regional mass vaccination campaigns to reduce further spread of those serogroups.
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Bocharova Y, Chebotar I, Savinova T, Lyamin A, Kondratenko O, Polikarpova S, Fedorova N, Semykin S, Korostin D, Chaplin A, Shagin D, Mayanskiy N. Clonal diversity, antimicrobial resistance, and genome features among nonfermenting gram-negative bacteria isolated from patients with cystic fibrosis in Russia. Diagn Microbiol Infect Dis 2024; 108:116102. [PMID: 37984108 DOI: 10.1016/j.diagmicrobio.2023.116102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/29/2023] [Accepted: 10/06/2023] [Indexed: 11/22/2023]
Abstract
Nonfermenting gram-negative (NFGN) bacteria were isolated from cystic fibrosis (CF) patients and subjected to susceptibility testing and whole-genome sequencing. Among 170 enrolled CF patients, 112 (65.9%) were colonized with at least 1 key NFGN species. The species-specific infection rate was highest for Pseudomonas aeruginosa (40.6%) followed by Stenotrophomonas maltophilia (14.1%), Achromobacter spp. (9.4%), and Burkholderia cepacia complex (Bcc, 8.2%) demonstrating a significant age-dependent increase for P. aeruginosa and Achromobacter spp., but not for S. maltophilia or Bcc. P. aeruginosa sequence types (STs) related to high-risk epidemic and global CF clones were carried by 12 (7.1%) and 13 (7.6%) patients, respectively. In total, 47% NFGN isolates, predominantly P. aeruginosa, harbored at least 1 plasmid-borne resistance gene; 5 ST235 isolates carried blaVIM2. Pathogenicity island-borne virulence genes were harbored by 9% NFGN isolates. These findings in conjunction with frequent early colonization by Bcc raised serious concerns regarding infection control in Russian CF centers.
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Affiliation(s)
- Yuliya Bocharova
- Pirogov Russian National Research Medical University, Moscow, Russia.
| | - Igor Chebotar
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Tatiana Savinova
- Pirogov Russian National Research Medical University, Moscow, Russia
| | | | | | | | - Natalia Fedorova
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Sergey Semykin
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitriy Korostin
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Andrey Chaplin
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitriy Shagin
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Nikolay Mayanskiy
- Pirogov Russian National Research Medical University, Moscow, Russia
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Mokaddas E, Asadzadeh M, Syed S, Albert MJ. High Prevalence of Novel Sequence Types in Streptococcus pneumoniae That Caused Invasive Diseases in Kuwait in 2018. Microorganisms 2024; 12:225. [PMID: 38276209 PMCID: PMC10819824 DOI: 10.3390/microorganisms12010225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND Multilocus sequence typing (MLST) is used to gain insight into the population genetics of bacteria in the form of sequence type (ST). MLST has been used to study the evolution and spread of virulent clones of Streptococcus pneumoniae in many parts of the world. Such data for S. pneumoniae are lacking for the countries of the Arabian Peninsula, including Kuwait. METHODS We determined the STs of all 31 strains of S. pneumoniae from invasive diseases received at a reference laboratory from various health centers in Kuwait during 2018 by MLST. The relationship among the isolates was determined by phylogenetic analysis. We also determined the serotypes by Quellung reaction, and antimicrobial susceptibility by Etest, against 15 antibiotics belonging to 10 classes. RESULTS There were 28 STs among the 31 isolates, of which 14 were new STs (45.2%) and 5 were rare STs (16.1%). Phylogenetic analysis revealed that 26 isolates (83.9%) were unrelated singletons, and the Kuwaiti isolates were related to those from neighboring countries whose information was gleaned from unpublished data available at the PubMLST website. Many of our isolates were resistant to penicillin, erythromycin, and azithromycin, and some were multidrug-resistant. Virulent serotype 8-ST53, and serotype 19A with new STs, were detected. CONCLUSIONS Our study detected an unusually large number of novel STs, which may indicate that Kuwait provides a milieu for the evolution of novel STs. Novel STs may arise due to recombination and can result in capsular switching. This can impact the effect of vaccination programs on the burden of invasive pneumococcal disease. This first report from the Arabian Peninsula justifies the continuous monitoring of S. pneumoniae STs for the possible evolution of new virulent clones and capsular switching.
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Affiliation(s)
| | | | | | - M. John Albert
- Department of Microbiology, College of Medicine, Kuwait University, P.O. Box 24923, Safat 13110, Kuwait; (E.M.); (M.A.); (S.S.)
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Cureño-Díaz MA, Plascencia-Nieto ES, Loyola-Cruz MÁ, Cruz-Cruz C, Nolasco-Rojas AE, Durán-Manuel EM, Ibáñez-Cervantes G, Gómez-Zamora E, Tamayo-Ordóñez MC, Tamayo-Ordóñez YDJ, Calzada-Mendoza CC, Bello-López JM. Gram-Negative ESKAPE Bacteria Surveillance in COVID-19 Pandemic Exposes High-Risk Sequence Types of Acinetobacter baumannii MDR in a Tertiary Care Hospital. Pathogens 2024; 13:50. [PMID: 38251357 PMCID: PMC10820853 DOI: 10.3390/pathogens13010050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/21/2023] [Accepted: 12/30/2023] [Indexed: 01/23/2024] Open
Abstract
The interruption of bacteriological surveillance due to the COVID-19 pandemic brought serious consequences, such as the collapse of health systems and the possible increase in antimicrobial resistance. Therefore, it is necessary to know the rate of resistance and its associated mechanisms in bacteria causing hospital infections during the pandemic. The aim of this work was to show the phenotypic and molecular characteristics of antimicrobial resistance in ESKAPE bacteria in a Mexican tertiary care hospital in the second and third years of the pandemic. For this purpose, during 2021 and 2022, two hundred unduplicated strains of the ESKAPE group (Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii) were collected from various clinical sources and categorized by resistance according to the CLSI. An analysis of variance (ANOVA) complemented by the Tukey test was performed to search for changes in antimicrobial susceptibility profiles during the study period. Finally, the mechanisms of resistance involved in carbapenem resistance were analyzed, and the search for efflux pumps and high-risk sequence types in A. baumannii was performed by multilocus analysis (MLST). The results showed no changes in K. pneumoniae resistance during the period analyzed. Decreases in quinolone resistance were identified in E. coli (p = 0.039) and P. aeruginosa (p = 0.03). Interestingly, A. baumannii showed increases in resistance to penicillins (p = 0.004), aminoglycosides (p < 0.001, p = 0.027), carbapenems (p = 0.027), and folate inhibitors (p = 0.001). Several genes involved in carbapenem resistance were identified (blaNDM, blaVIM, blaOXA, blaKPC, blaOXA-40, and blaOXA-48) with a predominance of blaOXA-40 and the adeABCRS efflux pump in A. baumannii. Finally, MLST analysis revealed the presence of globally distributed sequence types (ST369 and ST758) related to hospital outbreaks in other parts of the world. The results presented demonstrate that the ESKAPE group has played an important role during the COVID-19 pandemic as nosocomial antibiotic-resistant pathogens and in particular A. baumannii MDR as a potential reservoir of resistance genes. The implications of the increases in antimicrobial resistance in pathogens of the ESKAPE group and mainly in A. baumannii during the COVID-19 pandemic are analyzed and discussed.
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Affiliation(s)
- Mónica Alethia Cureño-Díaz
- Hospital Juárez de México, Mexico City 07760, Mexico
- Facultad de Ciencias de la Salud, Doctorado en Ciencias de la Salud, Universidad Anáhuac, Naucalpan de Juárez 52786, Mexico
| | - Estibeyesbo Said Plascencia-Nieto
- Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | | | - Clemente Cruz-Cruz
- Hospital Juárez de México, Mexico City 07760, Mexico
- Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Andres Emmanuel Nolasco-Rojas
- Hospital Juárez de México, Mexico City 07760, Mexico
- Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Emilio Mariano Durán-Manuel
- Hospital Juárez de México, Mexico City 07760, Mexico
- Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Gabriela Ibáñez-Cervantes
- Hospital Juárez de México, Mexico City 07760, Mexico
- Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | | | - María Concepción Tamayo-Ordóñez
- Laboratorio de Ingeniería Genética, Departamento de Biotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Coahuila, Coahuila 25280, Mexico
| | - Yahaira de Jesús Tamayo-Ordóñez
- Laboratorio de Biotecnología Ambiental, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico
| | - Claudia Camelia Calzada-Mendoza
- Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City 11340, Mexico
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Laklaeng SN, Phu DH, Songsri J, Wisessombat S, Mala W, Senghoi W, Phothaworn P, Nuinoon M, Wongtawan T, Klangbud WK. A systematic review and meta-analysis of the global prevalence and relationships among Burkholderia pseudomallei sequence types isolated from humans, animals, and the environment. Vet World 2024; 17:26-36. [PMID: 38406370 PMCID: PMC10884566 DOI: 10.14202/vetworld.2024.26-36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 12/08/2023] [Indexed: 02/27/2024] Open
Abstract
Background and Aim Burkholderia pseudomallei, a highly pathogenic bacterium responsible for melioidosis, exhibits ecological ubiquity and thrives within soil and water reservoirs, posing significant infection risks to humans and animals through direct contact. The aim of this study was to elucidate the genetic diversity and prevalence patterns of B. pseudomallei sequence types (STs) across a global spectrum and to understand the relationships between strains isolated from different sources. Materials and Methods We performed a systematic review and meta-analysis in this study. Extensive research was carried out across three comprehensive databases, including PubMed, Scopus, and ScienceDirect with data collected from 1924 to 2023. Results A total of 40 carefully selected articles contributed 2737 B. pseudomallei isolates attributed to 729 distinct STs and were incorporated into the systematic review. Among these, ST46 emerged as the most prominent, featuring in 35% of the articles and demonstrating a dominant prevalence, particularly within Southeast Asia. Moreover, ST51 consistently appeared across human, animal, and environmental studies. Subsequently, we performed a meta-analysis, focusing on nine specific STs: ST46, ST51, ST54, ST70, ST84, ST109, ST289, ST325, and ST376. Surprisingly, no statistically significant differences in their pooled prevalence proportions were observed across these compartments for ST46, ST70, ST289, ST325, and ST376 (all p > 0.69). Conversely, the remaining STs, including ST51, ST54, ST84, and ST109, displayed notable variations in their prevalence among the three domains (all p < 0.04). Notably, the pooled prevalence of ST51 in animals and environmental samples surpassed that found in human isolates (p < 0.01). Conclusion To the best of our knowledge, this study is the first systematic review and meta-analysis to investigate the intricate relationships between STs and their sources and contributes significantly to our understanding of B. pseudomallei diversity within the One Health framework.
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Affiliation(s)
- Sa-ngob Laklaeng
- College of Graduate Studies, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Doan Hoang Phu
- College of Graduate Studies, Walailak University, Nakhon Si Thammarat 80160, Thailand
- Faculty of Animal Science and Veterinary Medicine, Nong Lam University, Ho Chi Minh City 70000, Vietnam
| | - Jirarat Songsri
- Center of Excellence in Research for Melioidosis and Microorganisms, Walailak University, Nakhon Si Thammarat 80160, Thailand
- Department of Medical Technology, School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Sueptrakool Wisessombat
- Center of Excellence in Research for Melioidosis and Microorganisms, Walailak University, Nakhon Si Thammarat 80160, Thailand
- Department of Medical Technology, School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Wanida Mala
- Center of Excellence in Research for Melioidosis and Microorganisms, Walailak University, Nakhon Si Thammarat 80160, Thailand
- Department of Medical Technology, School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Wilaiwan Senghoi
- Center of Excellence in Research for Melioidosis and Microorganisms, Walailak University, Nakhon Si Thammarat 80160, Thailand
- Department of Medical Technology, School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Preeda Phothaworn
- Center of Excellence in Research for Melioidosis and Microorganisms, Walailak University, Nakhon Si Thammarat 80160, Thailand
- Department of Medical Technology, School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Manit Nuinoon
- Department of Medical Technology, School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Tuempong Wongtawan
- Akkhraratchakumari Veterinary College, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Wiyada Kwanhian Klangbud
- Center of Excellence in Research for Melioidosis and Microorganisms, Walailak University, Nakhon Si Thammarat 80160, Thailand
- Department of Medical Technology, School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat 80160, Thailand
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Malaure C, Geslain G, Birgy A, Bidet P, Poilane I, Allain M, Liberge M, Khattat N, Sikias P, Bonacorsi S. Early-Onset Infection Caused by Escherichia coli Sequence Type 1193 in Late Preterm and Full-Term Neonates. Emerg Infect Dis 2024; 30:20-28. [PMID: 38146959 PMCID: PMC10756391 DOI: 10.3201/eid3001.230851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023] Open
Abstract
Using whole-genome sequencing, we characterized Escherichia coli strains causing early-onset sepsis (EOS) in 32 neonatal cases from a 2019-2021 prospective multicenter study in France and compared them to E. coli strains collected from vaginal swab specimens from women in third-trimester gestation. We observed no major differences in phylogenetic groups or virulence profiles between the 2 collections. However, sequence type (ST) analysis showed the presence of 6/32 (19%) ST1193 strains causing EOS, the same frequency as in the highly virulent clonal group ST95. Three ST1193 strains caused meningitis, and 3 harbored extended-spectrum β-lactamase. No ST1193 strains were isolated from vaginal swab specimens. Emerging ST1193 appears to be highly prevalent, virulent, and antimicrobial resistant in neonates. However, the physiopathology of EOS caused by ST1193 has not yet been elucidated. Clinicians should be aware of the possible presence of E. coli ST1193 in prenatal and neonatal contexts and provide appropriate monitoring and treatment.
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Beig M, Badmasti F, Solgi H, Nikbin VS, Sholeh M. Carbapenemase genes distribution in clonal lineages of Acinetobacter baumannii: a comprehensive study on plasmids and chromosomes. Front Cell Infect Microbiol 2023; 13:1283583. [PMID: 38106472 PMCID: PMC10722191 DOI: 10.3389/fcimb.2023.1283583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 11/14/2023] [Indexed: 12/19/2023] Open
Abstract
Background The global spread of plasmids carrying carbapenemase genes within carbapenem resistant Acinetobacter baumannii (CRAB) strains poses a worldwide public health issue. In this study, we conducted a comprehensive genetic analysis of plasmids and chromosomes harboring the major carbapenemase genes (bla NDM, bla KPC, bla VIM, bla IMP, bla GES, bla OXA-58-like, bla OXA-24/40-like, bla OXA-143-like, and bla OXA-23-like) in CRAB strains using bioinformatic tools. Methods We retrieved plasmids and chromosomes carrying the major carbapenemase genes from GenBank. The size, replicon type, and conjugal apparatus of the plasmids were also determined. Furthermore, allele types, co-existence of other antimicrobial resistance genes alongside carbapenemases in plasmids or chromosomes, co-occurrence of carbapenemase genes, gene repetition, and sequence types (ST) of whole genomes were characterized. Results The database contained 113 plasmids and 38 chromosomes harboring carbapenemase genes. This investigation revealed that bla NDM and bla OXA-58-like were the predominant allele types in both the plasmids and chromosomes. Nine (7.96%) plasmids with bla NDM-1 were potentially conjugative. The most common replicon types of the plasmids were R3-T1, R3-T8, R3-T2, R3-T23, and RP-T1. The analysis revealed that bla NDM-1 and bla OXA-58-like genes possessed the highest variety of co-existence with other antibiotic resistance genes. The co-occurrence of dual carbapenemases was identified in 12 plasmids and 19 chromosomes. Carbapenemase gene repetitions were identified in 10 plasmids and one chromosome. Circular alignment revealed that the plasmids carrying the co-occurrence of bla NDM-1 and bla OXA-58 were more homogeneous. However, there was heterogeneity in certain regions of these plasmids. According to the minimum spanning tree (MST) results, the majority of the plasmids belonged to the genomes of ST2Pas, ST1Pas, ST422Pas, ST622Pas, and ST85Pas. Conclusion A. baumannii appears to have a strong ability for genome plasticity to incorporate carbapenemase genes on its plasmids and chromosomes to develop resistance against carbapenems. Mobilizable plasmids harboring carbapenemases significantly contribute to the dissemination of these genes. The genetic structure of the plasmids revealed a strong associations of class I integrons, ISAba-like structures, Tn4401 elements, and aac (6')-Ib with carbapenemases. Furthermore, gene repetition may also be associated with carbapenem heteroresistance.
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Affiliation(s)
- Masoumeh Beig
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Farzad Badmasti
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Hamid Solgi
- Isfahan Endocrine and Metabolism Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | | | - Mohammad Sholeh
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
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Zouharová M, Matiašovic J, Gebauer J, Matiašková K, Nedbalcová K. Survey of Genotype Diversity, Virulence, and Antimicrobial Resistance Genes in Mastitis-Causing Streptococcus uberis in Dairy Herds Using Whole-Genome Sequencing. Pathogens 2023; 12:1378. [PMID: 38133263 PMCID: PMC10745719 DOI: 10.3390/pathogens12121378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 11/18/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023] Open
Abstract
Streptococcus uberis is one of the primary causative agents of mastitis, a clinically and economically significant disease that affects dairy cattle worldwide. In this study, we analyzed 140 S. uberis strains isolated from mastitis milk samples collected from 74 cow herds in the Czech Republic. We employed whole-genome sequencing to screen for the presence of antimicrobial resistance (AMR) genes and genes encoding virulence factors, and to assess their genetic relationships. Our analysis revealed the presence of 88 different sequence types (STs), with 41% of the isolates assigned to global clonal complexes (GCCs), the majority of which were affiliated with GCC5. The STs identified were distributed across the major phylogenetic branches of all currently known STs. We identified fifty-one putative virulence factor genes, and the majority of isolates carried between 27 and 29 of these genes. A tendency of virulence factors and AMR genes to cluster with specific STs was observed, although such clustering was not evident within GCCs. Principal component analysis did not reveal significant diversity among isolates when grouped by GCC or ST prevalence. The substantial genomic diversity and the wide array of virulence factors found in S. uberis strains present a challenge for the implementation of effective anti-mastitis measures.
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Affiliation(s)
- Monika Zouharová
- Department of Infectious Diseases and Preventive Medicine, Veterinary Research Institute, 62100 Brno, Czech Republic; (J.M.); (J.G.); (K.M.); (K.N.)
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Takahashi H, Morita M, Kamiya H, Fukusumi M, Yasuda M, Sunagawa M, Nakamura-Miwa H, Ohama Y, Shimuta K, Ohnishi M, Saito R, Akeda Y. Emergence of ciprofloxacin- and penicillin-resistant Neisseria meningitidis isolates in Japan between 2003 and 2020 and its genetic features. Antimicrob Agents Chemother 2023; 67:e0074423. [PMID: 37874301 PMCID: PMC10648979 DOI: 10.1128/aac.00744-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/28/2023] [Indexed: 10/25/2023] Open
Abstract
Although we previously reported that some meningococcal isolates in Japan were resistant to penicillin (PCG) and ciprofloxacin (CIP), the antibiotic susceptibilities of Neisseria meningitidis isolates obtained in Japan remained unclear. In the present study, 290 N. meningitidis isolates in Japan between 2003 and 2020 were examined for the sensitivities to eight antibiotics (azithromycin, ceftriaxone, ciprofloxacin, chloramphenicol, meropenem, minocycline, penicillin, and rifampicin). All isolates were susceptible to chloramphenicol, ceftriaxone, meropenem, minocycline, and rifampicin while two were resistant to azithromycin. Penicillin- and ciprofloxacin-resistant and -intermediate isolates (PCGR, CIPR, PCGI and CIPI, respectively) were also identified. Based on our previous findings from whole genome sequence analysis, approximately 40% of PCGI were associated with ST-11026 and cc2057 meningococci, both of which were unique to Japan. Moreover, the majority of ST-11026 meningococci were CIPR or CIPI. Sensitivities to PCG and CIP were closely associated with genetic features, which indicated that, at least for Japanese meningococcal isolates, PCGR/I or CIPI/R would be less likely to be horizontally conferred from other neisserial genomes by transferring of the genes responsible (penA and gyrA genes, respectively), but rather that ancestral N. meningitidis strains conferring PCGR/I or CIPI/R phenotypes clonally disseminated in Japan.
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Affiliation(s)
- Hideyuki Takahashi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Masatomo Morita
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hajime Kamiya
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Munehisa Fukusumi
- Center for Field Epidemic Intelligence, Research and Professional Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Mitsuru Yasuda
- Department of Infection Control and Laboratory Medicine, Sapporo Medical University, Sapporo, Japan
| | - Masatomi Sunagawa
- Center for Field Epidemic Intelligence, Research and Professional Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Haruna Nakamura-Miwa
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yuki Ohama
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Ken Shimuta
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Ryoichi Saito
- Department of Molecular Microbiology Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yukihiro Akeda
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
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Zhang P, Wu W, Wang N, Feng H, Wang J, Wang F, Zhang Y, Chen H, Yang Q, Jiang Y, Qu T. Pseudomonas aeruginosa High-Risk Sequence Type 463 Co-Producing KPC-2 and AFM-1 Carbapenemases, China, 2020-2022. Emerg Infect Dis 2023; 29:2136-2140. [PMID: 37735755 PMCID: PMC10521588 DOI: 10.3201/eid2910.230509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023] Open
Abstract
We report the clonal spread and evolution of high-risk Pseudomonas aeruginosa sequence type 463 co-producing KPC-2 and AFM-1 carbapenemases isolated from hospital patients in China during 2020-2022. Those strains pose a substantial public health threat and surveillance and stricter infection-control measures are essential to prevent further infections.
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Affiliation(s)
| | | | - Nanfei Wang
- The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China (P. Zhang, W. Wu, N. Wang, H. Feng, J. Wang, F. Wang, Y. Zhang, H. Chen, Q. Yang, T. Qu)
- Zhejiang University School of Medicine Sir Run Run Shaw Hospital, Hangzhou (Y. Jiang)
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou (Y. Jiang)
| | - Haiting Feng
- The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China (P. Zhang, W. Wu, N. Wang, H. Feng, J. Wang, F. Wang, Y. Zhang, H. Chen, Q. Yang, T. Qu)
- Zhejiang University School of Medicine Sir Run Run Shaw Hospital, Hangzhou (Y. Jiang)
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou (Y. Jiang)
| | - Jie Wang
- The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China (P. Zhang, W. Wu, N. Wang, H. Feng, J. Wang, F. Wang, Y. Zhang, H. Chen, Q. Yang, T. Qu)
- Zhejiang University School of Medicine Sir Run Run Shaw Hospital, Hangzhou (Y. Jiang)
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou (Y. Jiang)
| | - Fang Wang
- The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China (P. Zhang, W. Wu, N. Wang, H. Feng, J. Wang, F. Wang, Y. Zhang, H. Chen, Q. Yang, T. Qu)
- Zhejiang University School of Medicine Sir Run Run Shaw Hospital, Hangzhou (Y. Jiang)
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou (Y. Jiang)
| | - Yan Zhang
- The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China (P. Zhang, W. Wu, N. Wang, H. Feng, J. Wang, F. Wang, Y. Zhang, H. Chen, Q. Yang, T. Qu)
- Zhejiang University School of Medicine Sir Run Run Shaw Hospital, Hangzhou (Y. Jiang)
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou (Y. Jiang)
| | - Hongchao Chen
- The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China (P. Zhang, W. Wu, N. Wang, H. Feng, J. Wang, F. Wang, Y. Zhang, H. Chen, Q. Yang, T. Qu)
- Zhejiang University School of Medicine Sir Run Run Shaw Hospital, Hangzhou (Y. Jiang)
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou (Y. Jiang)
| | - Qing Yang
- The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China (P. Zhang, W. Wu, N. Wang, H. Feng, J. Wang, F. Wang, Y. Zhang, H. Chen, Q. Yang, T. Qu)
- Zhejiang University School of Medicine Sir Run Run Shaw Hospital, Hangzhou (Y. Jiang)
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou (Y. Jiang)
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11
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Riquelme MP, Martinez RW, Brito B, García P, Legarraga P, Wozniak A. Chromosome-Mediated Colistin Resistance in Clinical Isolates of Klebsiella pneumoniae and Escherichia coli: Mutation Analysis in the Light of Genetic Background. Infect Drug Resist 2023; 16:6451-6462. [PMID: 37789836 PMCID: PMC10544214 DOI: 10.2147/idr.s427398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 08/10/2023] [Indexed: 10/05/2023] Open
Abstract
Purpose Colistin resistance mechanisms involving mutations in chromosomal genes associated with LPS modification are not completely understood. Mutations in genes coding for the MgrB regulator frequently account for colistin resistance in Klebsiella pneumoniae, whereas mutations in genes coding for PhoPQ and PmrAB are frequent in E. coli. Our aim was to perform a genetic analysis of chromosomal mutations in colistin-resistant (MIC ≥4 µg/mL) clinical isolates of K. pneumoniae (n = 8) and E. coli (n = 7) of different STs. Methods Isolates were obtained in a 3-year period in a university hospital in Santiago, Chile. Susceptibility to colistin, aminoglycosides, cephalosporins, carbapenems and ciprofloxacin was determined through broth microdilution. Whole genome sequencing was performed for all isolates and chromosomal gene sequences were compared with sequences of colistin-susceptible isolates of the same sequence types. Results None of the isolates carried mcr genes. Most of the isolates were susceptible to all the antibiotics analyzed. E. coli isolates were ST69, ST127, ST59, ST131 and ST14, and K. pneumoniae isolates were ST454, ST45, ST6293, ST380 and ST25. All the isolates had mutations in chromosomal genes analyzed. K. pneumoniae had mutations mainly in mgrB gene, whereas E. coli had mutations in pmrA, pmrB and pmrE genes. Most of the amino acid changes in LPS-modifying enzymes of colistin-resistant isolates were found in colistin-susceptible isolates of the same and/or different ST. Eleven of them were found only in colistin-resistant isolates. Conclusion Colistin resistance mechanisms depend on genetic background, and are due to chromosomal mutations, which implies a lower risk of transmission than plasmid-mediated genes. Colistin resistance is not associated with multidrug-resistance, nor to high-risk sequence types.
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Affiliation(s)
- María Paz Riquelme
- Department of Clinical Laboratories - School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Rodrigo W Martinez
- Genomics & Resistant Microbes Group (Germ) - Instituto de Ciencias e Innovación en Medicina (ICIM); School of Medicine-Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
- Millennium Nucleus for Collaborative Research on Bacterial Resistance (MICROB-R), SantiagoChile
| | - Bárbara Brito
- Australian Institute for Microbiology & Infection - Faculty of Science, University of Technology Sydney, Sydney, Australia
| | - Patricia García
- Department of Clinical Laboratories - School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Millennium Nucleus for Collaborative Research on Bacterial Resistance (MICROB-R), SantiagoChile
- Clinical Laboratories Network, Red de Salud UC-CHRISTUS, Santiago, Chile
| | - Paulette Legarraga
- Department of Clinical Laboratories - School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Clinical Laboratories Network, Red de Salud UC-CHRISTUS, Santiago, Chile
| | - Aniela Wozniak
- Department of Clinical Laboratories - School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Millennium Nucleus for Collaborative Research on Bacterial Resistance (MICROB-R), SantiagoChile
- Clinical Laboratories Network, Red de Salud UC-CHRISTUS, Santiago, Chile
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12
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Fuzi M, Sokurenko E. Commensal Fitness Advantage May Contribute to the Global Dissemination of Multidrug-Resistant Lineages of Bacteria-The Case of Uropathogenic E. coli. Pathogens 2023; 12:1150. [PMID: 37764958 PMCID: PMC10536240 DOI: 10.3390/pathogens12091150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/01/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
It is widely accepted that favorable fitness in commensal colonization is one of the prime facilitators of clonal dissemination in bacteria. The question arises as to what kind of fitness advantage may be wielded by uropathogenic strains of the two predominant fluoroquinolone- and multidrug-resistant clonal groups of E. coli-ST131-H30 and ST1193, which has permitted their unprecedented pandemic-like global expansion in the last few decades. The colonization-associated genes' content, carriage of low-cost plasmids, and integrons with weak promoters could certainly contribute to the fitness of the pandemic groups, although those genetic factors are common among other clonal groups as well. Also, ST131-H30 and ST1193 strains harbor fluoroquinolone-resistance conferring mutations targeting serine residues in DNA gyrase (GyrA-S83) and topoisomerase IV (ParC-S80) that, in those clonal backgrounds, might result in a commensal fitness benefit, i.e., beyond the antibiotic resistance per se. This fitness gain might have contributed not only to the widespread dissemination of these major clones in the healthcare setting but also to their long-term colonization of healthy individuals and, thus, circulation in the community, even in a low or no fluoroquinolone use environment. This evolutionary shift affecting commensal E. coli, initiated by mutations co-favorable in both antibiotics-treated patients and healthy individuals warrants more in-depth studies to monitor further changes in the epidemiological situation and develop effective measures to reduce the antibiotic resistance spread.
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Affiliation(s)
- Miklos Fuzi
- Independent Researcher, Seattle, WA 98195, USA
| | - Evgeni Sokurenko
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA 98195, USA;
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13
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Gana J, Gcebe N, Pierneef RE, Chen Y, Moerane R, Adesiyun AA. Genomic Characterization of Listeria innocua Isolates Recovered from Cattle Farms, Beef Abattoirs, and Retail Outlets in Gauteng Province, South Africa. Pathogens 2023; 12:1062. [PMID: 37624022 PMCID: PMC10457781 DOI: 10.3390/pathogens12081062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 08/12/2023] [Accepted: 08/15/2023] [Indexed: 08/26/2023] Open
Abstract
Whole-genome sequencing (WGS) was used for the genomic characterization of one hundred and ten strains of Listeria innocua (L. innocua) isolated from twenty-three cattle farms, eight beef abattoirs, and forty-eight retail outlets in Gauteng province, South Africa. In silico multilocus sequence typing (MLST) was used to identify the isolates' sequence types (STs). BLAST-based analyses were used to identify antimicrobial and virulence genes. The study also linked the detection of the genes to the origin (industries and types of samples) of the L. innocua isolates. The study detected 14 STs, 13 resistance genes, and 23 virulence genes. Of the 14 STs detected, ST637 (26.4%), ST448 (20%), 537 (13.6%), and 1085 (12.7%) were predominant, and the frequency varied significantly (p < 0.05). All 110 isolates of L. innocua were carriers of one or more antimicrobial resistance genes, with resistance genes lin (100%), fosX (100%), and tet(M) (30%) being the most frequently detected (p < 0.05). Of the 23 virulence genes recognized, 13 (clpC, clpE, clpP, hbp1, svpA, hbp2, iap/cwhA, lap, lpeA, lplA1, lspA, oatA, pdgA, and prsA2) were found in all 110 isolates of L. innocua. Overall, diversity and significant differences were detected in the frequencies of STs, resistance, and virulence genes according to the origins (source and sample type) of the L. innocua isolates. This, being the first genomic characterization of L. innocua recovered from the three levels/industries (farm, abattoir, and retail) of the beef production system in South Africa, provides data on the organism's distribution and potential food safety implications.
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Affiliation(s)
- James Gana
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Onderstepoort 0110, South Africa; (J.G.); (R.M.)
- Agricultural Education, Federal College of Education, Kontagora 923101, Nigeria
| | - Nomakorinte Gcebe
- Bacteriology Department, Onderstepoort Veterinary Research, Agricultural Research Council, Pretoria 0110, South Africa;
| | - Rian Ewald Pierneef
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0001, South Africa;
- Centre for Bioinformatics and Computational Biology, University of Pretoria, Pretoria 0001, South Africa
- Microbiome@UP, Department of Biochemistry, Genetics, and Microbiology, University of Pretoria, Pretoria 0001, South Africa
| | - Yi Chen
- Center for Food Safety and Applied Nutrition, US Food and Drug Administration, 5001 Campus Dr. Room 4E-007/Mailstop HFS-710, College Park, MD 20740, USA;
| | - Rebone Moerane
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Onderstepoort 0110, South Africa; (J.G.); (R.M.)
| | - Abiodun Adewale Adesiyun
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Onderstepoort 0110, South Africa; (J.G.); (R.M.)
- School of Veterinary Medicine, Faculty of Medical Sciences, University of the West Indies, St. Augustine 685509, Trinidad and Tobago
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14
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Richards GP, Watson MA, Williams HN, Jones JL. Predator-Prey Interactions between Halobacteriovorax and Pathogenic Vibrio parahaemolyticus Strains: Geographical Considerations and Influence of Vibrio Hemolysins. Microbiol Spectr 2023; 11:e0235323. [PMID: 37409976 PMCID: PMC10434201 DOI: 10.1128/spectrum.02353-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 06/23/2023] [Indexed: 07/07/2023] Open
Abstract
Halobacteriovorax is a genus of naturally occurring marine predatory bacteria that attack, replicate within, and lyse vibrios and other bacteria. This study evaluated the specificity of four Halobacteriovorax strains against important sequence types (STs) of clinically relevant Vibrio parahaemolyticus, including pandemic strains ST3 and ST36. The Halobacteriovorax bacteria were previously isolated from seawater from the Mid-Atlantic, Gulf of Mexico, and Hawaiian coasts of the United States. Specificity screening was performed using a double agar plaque assay technique on 23 well-characterized and genomically sequenced V. parahaemolyticus strains isolated from infected individuals from widely varying geographic locations within the United States. With few exceptions, results showed that Halobacteriovorax bacteria were excellent predators of the V. parahaemolyticus strains regardless of the origins of the predator or prey. Sequence types and serotypes of V. parahaemolyticus did not influence host specificity, nor did the presence or absence of genes for the thermostable direct hemolysin (TDH) or the TDH-related hemolysin, although faint (cloudy) plaques were present when one or both hemolysins were absent in three of the Vibrio strains. Plaque sizes varied depending on both the Halobacteriovorax and Vibrio strains evaluated, suggesting differences in Halobacteriovorax replication and/or growth rates. The very broad infectivity of Halobacteriovorax toward pathogenic strains of V. parahaemolyticus makes Halobacteriovorax a strong candidate for use in commercial processing applications to enhance the safety of seafoods. IMPORTANCE Vibrio parahaemolyticus is a formidable obstacle to seafood safety. Strains pathogenic to humans are numerous and difficult to control, especially within molluscan shellfish. The pandemic spread of ST3 and ST36 has caused considerable concern, but many other STs are also problematic. The present study demonstrates broad predatory activity of Halobacteriovorax strains obtained along U.S. coastal waters from the Mid-Atlantic, Gulf Coast, and Hawaii toward strains of pathogenic V. parahaemolyticus. This broad activity against clinically relevant V. parahaemolyticus strains suggests a role for Halobacteriovorax in mediating pathogenic V. parahaemolyticus levels in seafoods and their environment as well as the potential application of these predators in the development of new disinfection technologies to reduce pathogenic vibrios in molluscan shellfish and other seafoods.
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Affiliation(s)
- Gary P. Richards
- U.S. Department of Agriculture, Agricultural Research Service, Delaware State University, Dover, Delaware, USA
| | - Michael A. Watson
- U.S. Department of Agriculture, Agricultural Research Service, Delaware State University, Dover, Delaware, USA
| | - Henry N. Williams
- School of the Environment, Florida Agricultural and Mechanical University, Tallahassee, Florida, USA
| | - Jessica L. Jones
- U.S. Food and Drug Administration, Division of Seafood Science and Technology, Gulf Coast Seafood Laboratory, Dauphin Island, Alabama, USA
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15
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Grattarola C, Petrella A, Lucifora G, Di Francesco G, Di Nocera F, Pintore A, Cocumelli C, Terracciano G, Battisti A, Di Renzo L, Farina D, Di Francesco CE, Crescio MI, Zoppi S, Dondo A, Iulini B, Varello K, Mignone W, Goria M, Mattioda V, Giorda F, Di Guardo G, Janowicz A, Tittarelli M, De Massis F, Casalone C, Garofolo G. Brucella ceti Infection in Striped Dolphins from Italian Seas: Associated Lesions and Epidemiological Data. Pathogens 2023; 12:1034. [PMID: 37623994 PMCID: PMC10459742 DOI: 10.3390/pathogens12081034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/10/2023] [Accepted: 08/10/2023] [Indexed: 08/26/2023] Open
Abstract
Brucella ceti infections have been increasingly reported in cetaceans. In this study, we analyzed all cases of B. ceti infection detected in striped dolphins stranded along the Italian coastline between 2012 and 2021 (N = 24). We focused on the pathogenic role of B. ceti through detailed pathological studies, and ad hoc microbiological, biomolecular, and serological investigations, coupled with a comparative genomic analysis of the strains. Neurobrucellosis was observed in 20 animals. The primary histopathologic features included non-suppurative meningoencephalitis (N = 9), meningitis (N = 6), and meningoencephalomyelitis (N = 5), which was also associated with typical lesions in other tissues (N = 8). Co-infections were detected in more than half of the cases, mostly involving Cetacean Morbillivirus (CeMV). The 24 B. ceti isolates were assigned primarily to sequence type 26 (ST26) (N = 21) and, in a few cases, ST49 (N = 3). The multilocus sequence typing (cgMLST) based on whole genome sequencing (WGS) data showed that strains from Italy clustered into four genetically distinct clades. Plotting these clades onto a geographic map suggests a link between their phylogeny and the topographical distribution. These results support the role of B. ceti as a primary neurotropic pathogen for striped dolphins and highlight the utility of WGS data in understanding the evolution of this emerging pathogen.
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Affiliation(s)
- Carla Grattarola
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Torino, Italy; (M.I.C.); (S.Z.); (A.D.); (B.I.); (K.V.); (W.M.); (M.G.); (V.M.); (F.G.); (C.C.)
| | - Antonio Petrella
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 71121 Foggia, Italy; (A.P.); (D.F.)
| | - Giuseppe Lucifora
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, 89852 Vibo Valentia, Italy;
| | - Gabriella Di Francesco
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, 64100 Teramo, Italy; (G.D.F.); (L.D.R.)
| | - Fabio Di Nocera
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, 80055 Portici, Italy;
| | - Antonio Pintore
- Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy;
| | - Cristiano Cocumelli
- Istituto Zooprofilattico del Lazio e della Toscana, 00178 Roma, Italy; (C.C.); (A.B.)
| | | | - Antonio Battisti
- Istituto Zooprofilattico del Lazio e della Toscana, 00178 Roma, Italy; (C.C.); (A.B.)
| | - Ludovica Di Renzo
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, 64100 Teramo, Italy; (G.D.F.); (L.D.R.)
| | - Donatella Farina
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 71121 Foggia, Italy; (A.P.); (D.F.)
| | | | - Maria Ines Crescio
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Torino, Italy; (M.I.C.); (S.Z.); (A.D.); (B.I.); (K.V.); (W.M.); (M.G.); (V.M.); (F.G.); (C.C.)
| | - Simona Zoppi
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Torino, Italy; (M.I.C.); (S.Z.); (A.D.); (B.I.); (K.V.); (W.M.); (M.G.); (V.M.); (F.G.); (C.C.)
| | - Alessandro Dondo
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Torino, Italy; (M.I.C.); (S.Z.); (A.D.); (B.I.); (K.V.); (W.M.); (M.G.); (V.M.); (F.G.); (C.C.)
| | - Barbara Iulini
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Torino, Italy; (M.I.C.); (S.Z.); (A.D.); (B.I.); (K.V.); (W.M.); (M.G.); (V.M.); (F.G.); (C.C.)
| | - Katia Varello
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Torino, Italy; (M.I.C.); (S.Z.); (A.D.); (B.I.); (K.V.); (W.M.); (M.G.); (V.M.); (F.G.); (C.C.)
| | - Walter Mignone
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Torino, Italy; (M.I.C.); (S.Z.); (A.D.); (B.I.); (K.V.); (W.M.); (M.G.); (V.M.); (F.G.); (C.C.)
| | - Maria Goria
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Torino, Italy; (M.I.C.); (S.Z.); (A.D.); (B.I.); (K.V.); (W.M.); (M.G.); (V.M.); (F.G.); (C.C.)
| | - Virginia Mattioda
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Torino, Italy; (M.I.C.); (S.Z.); (A.D.); (B.I.); (K.V.); (W.M.); (M.G.); (V.M.); (F.G.); (C.C.)
| | - Federica Giorda
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Torino, Italy; (M.I.C.); (S.Z.); (A.D.); (B.I.); (K.V.); (W.M.); (M.G.); (V.M.); (F.G.); (C.C.)
| | - Giovanni Di Guardo
- Faculty of Veterinary Medicine, University of Teramo, 64100 Teramo, Italy; (C.E.D.F.); (G.D.G.)
| | - Anna Janowicz
- National and OIE Reference Laboratory for Brucellosis, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, 64100 Teramo, Italy; (A.J.); (M.T.); (F.D.M.)
| | - Manuela Tittarelli
- National and OIE Reference Laboratory for Brucellosis, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, 64100 Teramo, Italy; (A.J.); (M.T.); (F.D.M.)
| | - Fabrizio De Massis
- National and OIE Reference Laboratory for Brucellosis, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, 64100 Teramo, Italy; (A.J.); (M.T.); (F.D.M.)
| | - Cristina Casalone
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Torino, Italy; (M.I.C.); (S.Z.); (A.D.); (B.I.); (K.V.); (W.M.); (M.G.); (V.M.); (F.G.); (C.C.)
| | - Giuliano Garofolo
- National and OIE Reference Laboratory for Brucellosis, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, 64100 Teramo, Italy; (A.J.); (M.T.); (F.D.M.)
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Abstract
Iron is essential for growth in most bacteria due to its redox activity and its role in essential metabolic reactions; it is a cofactor for many bacterial enzymes. The bacterium Acinetobacter baumannii is a multidrug-resistant nosocomial pathogen. A. baumannii responds to low iron availability imposed by the host through the exploitation of multiple iron-acquisition strategies, which are likely to deliver iron to the cell under a variety of environmental conditions, including human and animal infection. To date, six different gene clusters for active iron uptake have been described in A. baumannii , encoding protein systems involved in (i) ferrous iron uptake (feo ); (ii) haem uptake (hemT and hemO ); and (iii) synthesis and transport of the baumannoferrin(s) (bfn ), acinetobactin (bas /bau ) and fimsbactin(s) (fbs ) siderophores. Here we describe the structure, distribution and phylogeny of iron-uptake gene clusters among >1000 genotypically diverse A. baumannii isolates, showing that feo , hemT , bfn and bas /bau clusters are very prevalent across the dataset, whereas the additional haem-uptake system hemO is only present in a portion of the dataset and the fbs gene cluster is very rare. Since the expression of multiple iron-uptake clusters can be linked to virulence, the presence of the additional haem-uptake system hemO may have contributed to the success of some A. baumannii clones.
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Affiliation(s)
- Irene Artuso
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, Italy
| | - Harsh Poddar
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, Italy
| | - Benjamin A. Evans
- Norwich Medical School, University of East Anglia, Rosalind Franklin Road, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Paolo Visca
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, Italy
- Fondazione Santa Lucia IRCCS, Via Ardeatina, 306/354, 00179 Rome, Italy
- National Biodiversity Future Centre, Palermo 90133, Italy
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17
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Valciņa O, Pūle D, Ķibilds J, Labecka L, Terentjeva M, Krūmiņa A, Bērziņš A. Evaluation of Genetic Diversity and Virulence Potential of Legionella pneumophila Isolated from Water Supply Systems of Residential Buildings in Latvia. Pathogens 2023; 12:884. [PMID: 37513731 PMCID: PMC10385952 DOI: 10.3390/pathogens12070884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 06/21/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Legionella is an opportunistic pathogen with a biphasic life cycle that occasionally infects humans. The aim of the study was to assess the distribution of virulence genes and genetic diversity among L. pneumophila isolated from water supply systems of residential buildings in Latvia. In total, 492 water samples from 200 residential buildings were collected. Identification of Legionella spp. was performed according to ISO 11731, and 58 isolates were subjected to whole-genome sequencing. At least one Legionella-positive sample was found in 112 out of 200 apartment buildings (56.0%). The study revealed extensive sequence-type diversity, where 58 L. pneumophila isolates fell into 36 different sequence types. A total of 420 virulence genes were identified, of which 260 genes were found in all sequenced L. pneumophila isolates. The virulence genes enhC, htpB, omp28, and mip were detected in all isolates, suggesting that adhesion, attachment, and entry into host cells are enabled for all isolates. The relative frequency of virulence genes among L. pneumophila isolates was high. The high prevalence, extensive genetic diversity, and the wide range of virulence genes indicated that the virulence potential of environmental Legionella is high, and proper risk management is of key importance to public health.
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Affiliation(s)
- Olga Valciņa
- Institute of Food Safety, Animal Health and Environment "BIOR", LV-1076 Riga, Latvia
| | - Daina Pūle
- Institute of Food Safety, Animal Health and Environment "BIOR", LV-1076 Riga, Latvia
- Department of Water Engineering and Technology, Riga Technical University, LV-1048 Riga, Latvia
| | - Juris Ķibilds
- Institute of Food Safety, Animal Health and Environment "BIOR", LV-1076 Riga, Latvia
| | - Linda Labecka
- Institute of Food Safety, Animal Health and Environment "BIOR", LV-1076 Riga, Latvia
| | - Margarita Terentjeva
- Institute of Food and Environmental Hygiene, Faculty of Veterinary Medicine, Latvia University of Life Sciences and Technologies, LV-3004 Jelgava, Latvia
| | - Angelika Krūmiņa
- Department of Infectology, Riga Stradiņš University, LV-1007 Riga, Latvia
| | - Aivars Bērziņš
- Institute of Food Safety, Animal Health and Environment "BIOR", LV-1076 Riga, Latvia
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Chen CL, Janapatla RP, Dudek A, Chen YR, Lee HY, Chiu CH. Functional characterization and clinical implication of a novel epidemic carbapenem-resistant Acinetobacter baumannii genetic marker. Int J Antimicrob Agents 2023:106879. [PMID: 37290580 DOI: 10.1016/j.ijantimicag.2023.106879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 05/02/2023] [Accepted: 06/01/2023] [Indexed: 06/10/2023]
Abstract
OBJECTIVES The study aimed to evaluate the distribution and function of contact-dependent growth inhibition (CDI) systems associated with carbapenem-resistant Acinetobacter baumannii (CRAB) isolates. METHODS We examined these isolates by multilocus sequence typing (MLST) and PCR for the presence of CDI genes in CRAB and carbapenem-susceptible A. baumannii (CSAB) from patients with invasive disease in a medical center in Taiwan. Inter-bacterial competition assays were performed to characterize the in vitro function of the CDI system. RESULTS A total of 89 (61.0%) CSAB and 57 (39.0%) CRAB isolates were collected and examined. ST787 (20/57; 35.1%) was the most predominant sequence type among CRAB, followed by ST455 (10/57; 17.5%). More than half of the CRAB (56.1%, 32/57) belonged to CC455 and more than one third (38.6%, 22/57) to CC92. A novel CDI system, cdiTYTH1, was found in 87.7% (50/57) of the CRAB but only in 1.1% (1/89) of the CSAB isolates (P<0.00001). The cdiTYTH1 was also identified in 94.4% (17/18) of the previously genome-sequenced CRAB isolates and only one CSAB isolate from Taiwan. Two other previously reported CDI (cdi19606-1 and cdi19606-2) were not found in these isolates, except each in one CSAB. All 6 CRAB without cdiTYTH1 showed growth inhibition by a CSAB carrying cdiTYTH1 in vitro. All clinical CRAB isolates belonging to the predominant CC455 carried the newly identified cdiTYTH1. CONCLUSIONS This CDI system was widespread in CRAB clinical isolates and appeared to be an epidemic genetic marker for CRAB in Taiwan. The cdiTYTH1 was functional in vitro in bacterial competition assay.
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Affiliation(s)
- Chyi-Liang Chen
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Rajendra Prasad Janapatla
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Anna Dudek
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yan-Ru Chen
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Hao-Yuan Lee
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Department of Nursing, Jen-Teh Junior College of Medicine, Nursing and Management, Miaoli, Taiwan; Department of Pediatrics, Wei Gong Memorial Hospital, Miaoli, Taiwan; School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei, Taiwan.
| | - Cheng-Hsun Chiu
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan, Taiwan; Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan.
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19
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Agosta M, Bencardino D, Argentieri M, Pansani L, Sisto A, Ciofi Degli Atti ML, D'Amore C, Bagolan P, Iacobelli BD, Magnani M, Raponi M, Perno CF, Andreoni F, Bernaschi P. Clonal Spread of Hospital-Acquired NDM-1-Producing Klebsiella pneumoniae and Escherichia coli in an Italian Neonatal Surgery Unit: A Retrospective Study. Antibiotics (Basel) 2023; 12:antibiotics12040642. [PMID: 37107005 PMCID: PMC10135170 DOI: 10.3390/antibiotics12040642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/15/2023] [Accepted: 03/22/2023] [Indexed: 04/29/2023] Open
Abstract
This article reports a rapid and unexpected spread of colonization cases of NDM-1 carbapenemase-producing Klebsiella pneumoniae and Escherichia coli in a neonatal surgical unit (NSU) at Bambino Gesù Children's Hospital in Rome, Italy. Between the 16th of November 2020 and the 18th of January 2021, a total of 20 NDM-1 carbapenemase-producing K. pneumoniae (n = 8) and E. coli (n = 12) were isolated from 17 out of 230 stool samples collected from neonates admitted in the aforementioned ward and time period by an active surveillance culture program routinely in place to monitor the prevalence of colonization/infection with multidrug-resistant Gram-negative microorganisms. All strains were characterized by antimicrobial susceptibility testing, detection of resistance determinants, PCR-based replicon typing (PBRT) and multilocus-sequence typing (MLST). All isolates were highly resistant to most of the tested antibiotics, and molecular characterization revealed that all of them harbored the blaNDM-1 gene. Overall, IncA/C was the most common Inc group (n = 20/20), followed by IncFIA (n = 17/20), IncFIIK (n = 14/20) and IncFII (n = 11/20). MLST analysis was performed on all 20 carbapenemase-producing Enterobacterales (CPE) strains, revealing three different Sequence Types (STs) among E. coli isolates, with the prevalence of ST131 (n = 10/12; 83%). Additionally, among the 8 K. pneumoniae strains we found 2 STs with the prevalence of ST37 (n = 7/8; 87.5%). Although patient results were positive for CPE colonization during their hospital stay, infection control interventions prevented their dissemination in the ward and no cases of infection were recorded in the same time period.
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Affiliation(s)
- Marilena Agosta
- Microbiology and Diagnostic Immunology Unit, Department of Diagnostic and Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, 00163 Rome, Italy
| | - Daniela Bencardino
- Department of Biomolecular Sciences, University of Urbino "Carlo Bo", 61032 Fano, Italy
| | - Marta Argentieri
- Microbiology and Diagnostic Immunology Unit, Department of Diagnostic and Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, 00163 Rome, Italy
| | - Laura Pansani
- Microbiology and Diagnostic Immunology Unit, Department of Diagnostic and Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, 00163 Rome, Italy
| | - Annamaria Sisto
- Microbiology and Diagnostic Immunology Unit, Department of Diagnostic and Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, 00163 Rome, Italy
| | | | - Carmen D'Amore
- Clinical Pathways and Epidemiology Unit, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy
| | - Pietro Bagolan
- Neonatal Surgery Unit, Medical and Surgical Department of the Fetus-Newborn-Infant, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy
| | - Barbara Daniela Iacobelli
- Neonatal Surgery Unit, Medical and Surgical Department of the Fetus-Newborn-Infant, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy
| | - Mauro Magnani
- Department of Biomolecular Sciences, University of Urbino "Carlo Bo", 61032 Fano, Italy
| | - Massimiliano Raponi
- Health Directorate, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy
| | - Carlo Federico Perno
- Microbiology and Diagnostic Immunology Unit, Department of Diagnostic and Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, 00163 Rome, Italy
| | - Francesca Andreoni
- Department of Biomolecular Sciences, University of Urbino "Carlo Bo", 61032 Fano, Italy
- Clinical Pathology Unit, Azienda Sanitaria Territoriale, 61029 Urbino, Italy
| | - Paola Bernaschi
- Microbiology and Diagnostic Immunology Unit, Department of Diagnostic and Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, 00163 Rome, Italy
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20
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Salaheen S, Kim SW, Springer HR, Hovingh EP, Van Kessel JAS, Haley BJ. Characterization of Antimicrobial Resistance Genes and Virulence Factors in the Genomes of Escherichia coli ST69 Isolates from Preweaned Dairy Calves and Their Phylogenetic Relationship with Poultry and Human Clinical Strains. Microb Drug Resist 2023. [PMID: 36961425 DOI: 10.1089/mdr.2022.0266] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023] Open
Abstract
Escherichia coli sequence type 69 (ST69) are common causative agents of extraintestinal infections occurring in the bloodstream, cerebrospinal fluid, surgical sites, and, most frequently, the urinary tract. The objective of this study was to analyze the genomic characteristics of 45 antimicrobial-resistant Escherichia coli ST69 strains that were isolated from 28 calves on eight dairy farms in Pennsylvania, USA. The genomes were sequenced and the antimicrobial resistance genes (ARGs), virulence factors (VFs), and plasmid replicons were identified in silico. A phylogenetic analysis was conducted to compare these calf isolate genomes with poultry and human clinical E. coli ST69 genomes. In total, 23 ARGs, 45 VFs, and 15 plasmid replicons were identified. The majority of genomes (n = 36, 80%) had a multidrug-resistant (MDR) genotype and carried genes conferring resistance to antibiotics of human health significance. Phylogenetic analysis based on the core genomes revealed that calf isolates were nested within clades that included human and poultry isolates, indicating that they are not phylogenetically distinct. Results suggest that dairy calves are a reservoir of MDR E. coli ST69 strains with diverse ARG and VF profiles. This information will be helpful in assessing public health risks associated with E. coli ST69 in commercial dairy production systems.
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Affiliation(s)
- Serajus Salaheen
- Environmental Microbial and Food Safety Laboratory, United States Department of Agriculture, Beltsville Agricultural Research Center, Agricultural Research Service, Beltsville, Maryland, USA
| | - Seon Woo Kim
- Environmental Microbial and Food Safety Laboratory, United States Department of Agriculture, Beltsville Agricultural Research Center, Agricultural Research Service, Beltsville, Maryland, USA
| | - Hayley R Springer
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Ernest P Hovingh
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Jo Ann S Van Kessel
- Environmental Microbial and Food Safety Laboratory, United States Department of Agriculture, Beltsville Agricultural Research Center, Agricultural Research Service, Beltsville, Maryland, USA
| | - Bradd J Haley
- Environmental Microbial and Food Safety Laboratory, United States Department of Agriculture, Beltsville Agricultural Research Center, Agricultural Research Service, Beltsville, Maryland, USA
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21
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Fan S, Duan N, Chen W, Zhao X, Wang L, Du P, Guo J. Genomic Epidemiology of Streptococcus pneumoniae Isolated in a Tertiary Hospital in Beijing, China, from 2018 to 2022. Pathogens 2023; 12. [PMID: 36839557 DOI: 10.3390/pathogens12020284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/13/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
Streptococcus pneumoniae is one of the most common bacterial pathogens of a wide range of community-acquired infections. It has been more and more recognized that this bacterium could also play a role as a cause of nosocomial infections. In this study, by retrospective analysis of the phenotypic resistance characteristics and genomic characteristics of 52 S. pneumoniae isolates in a hospital in Beijing, China, from 2018 to 2022, we explored the carriage of resistance genes and mutations in penicillin-binding proteins corresponding to the resistances, and identified the population diversity based on the prediction of serotypes and identification of sequence types (STs). The isolates displayed resistances to erythromycin (98%), tetracycline (96%), sulfonamide (72%) and penicillin G (42%). Among the 52 isolates, 41 displayed multiple-drug resistance. In total, 37 STs and 21 serotypes were identified, and the clonal complex 271 serogroup 19 was the most prevalent subtype. Only 24 isolates (46.2%) of 7 serotypes were covered by the 13-valent pneumococcal conjugate vaccination. The isolates showed high carriages of resistance genes, including tet(M) (100%) and erm(B) (98.1%); additionally, 32 isolates (61.5%) had mutations in penicillin-binding proteins. We also observed 11 healthcare-associated infections and 3 cases infected by different subtypes of isolates. We did not find nosocomial transmissions between the patients, and these cases might be associated with the asymptomatic colonization of S. pneumoniae in the human population. Our results called for further active surveillance of these subtypes, as well as the continuous optimization of the treatment protocols.
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22
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Kong X, Chen T, Guo L, Zhou Y, Lu P, Xiao Y. Phenotypic and genomic comparison of dominant and nondominant sequence-type of Acinetobacter baumannii isolated in China. Front Cell Infect Microbiol 2023; 13:1118285. [PMID: 36891157 PMCID: PMC9986592 DOI: 10.3389/fcimb.2023.1118285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 01/31/2023] [Indexed: 02/22/2023] Open
Abstract
A. baumannii is a common clinical pathogen that often causes pneumonia and bloodstream infections in ICU patients. Sequence types (ST) are used to investigate the distribution and spread of A. baumannii. Biological characteristics such as virulence and resistance may play a role in A. baumannii becoming a specific dominant ST(DST,ST191, ST195 and ST208) strain. To characterize the biological, genetic, and transcriptomic differences between the DST and non-dominant ST(NST,ST462 and ST547,etc.) strains in A. baumannii, we performed several biological experiments and genetic, and transcriptomic analyses. The DST group displayed more resistance ability to desiccation, oxidation, multiple antibiotics, and complement killing than the NST group. However, the latter had higher biofilm formation ability than the former. The genomic analysis showed the DST group exhibited more capsule-related and aminoglycoside-resistant genes. Besides, GO analysis indicated that functions involved in lipid biosynthetic, transport, and the metabolic process were up-regulated in the DST group, while KEGG analysis manifested that the two-component system related to potassium ion transport and pili were down-regulated. In short, resistance to desiccation, oxidation, multiple antibiotics, and serum complement killing are important reasons for the formation of DST. Genes related to capsule synthesis and lipid biosynthesis and metabolism play an important role at the molecular level in the formation of DST.
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Affiliation(s)
- Xiaoyang Kong
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Tao Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lihua Guo
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yanzi Zhou
- Department of Rheumatology, Affiliated Hangzhou First People’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Ping Lu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yonghong Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
- *Correspondence: Yonghong Xiao,
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23
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Liu N, Liu D, Li K, Hu S, He Z. Pan-Genome Analysis of Staphylococcus aureus Reveals Key Factors Influencing Genomic Plasticity. Microbiol Spectr 2022; 10:e0311722. [PMID: 36318042 DOI: 10.1128/spectrum.03117-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The massive quantities of bacterial genomic data being generated have facilitated in-depth analyses of bacteria for pan-genomic studies. However, the pan-genome compositions of one species differed significantly between different studies, so we used Staphylococcus aureus as a model organism to explore the influences driving bacterial pan-genome composition. We selected a series of diverse strains for pan-genomic analysis to explore the pan-genomic composition of S. aureus at the species level and the actual contribution of influencing factors (sequence type [ST], source of isolation, country of isolation, and date of collection) to pan-genome composition. We found that the distribution of core genes in bacterial populations restrained under different conditions differed significantly and showed "local core gene regions" in the same ST. Therefore, we propose that ST may be a key factor driving the dynamic distribution of bacterial genomes and that phylogenetic analyses using whole-genome alignment are no longer appropriate in populations containing multiple ST strains. Pan-genomic analysis showed that some of the housekeeping genes of multilocus sequence typing (MLST) are carried at less than 60% in S. aureus strains. Consequently, we propose a new set of marker genes for the classification of S. aureus, which provides a reference for finding a new set of housekeeping genes to apply to MLST. In this study, we explored the role of driving factors influencing pan-genome composition, providing new insights into the study of bacterial pan-genomes. IMPORTANCE We sought to explore the impact of driving factors influencing pan-genome composition using Staphylococcus aureus as a model organism to provide new insights for the study of bacterial pan-genomes. We believe that the sequence type (ST) of the strains under consideration plays a significant role in the dynamic distribution of bacterial genes. Our findings indicate that there are a certain number of essential genes in Staphylococcus aureus; however, the number of core genes is not as high as previously thought. The new classification method proposed herein suggests that a new set of housekeeping genes more suitable for Staphylococcus aureus must be identified to improve the current classification status of this species.
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24
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Zouharová M, Šimek B, Gebauer J, Králová N, Kucharovičová I, Plodková H, Pecka T, Brychta M, Švejdová M, Nedbalcová K, Matiašková K, Matiašovic J. Characterisation of Streptococcus suis Isolates in the Czech Republic Collected from Diseased Pigs in the Years 2018-2022. Pathogens 2022; 12:pathogens12010005. [PMID: 36678353 PMCID: PMC9862946 DOI: 10.3390/pathogens12010005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/16/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022] Open
Abstract
As in other countries, in the Czech Republic, Streptococcus suis infection in pigs is considered an economically significant disease for the pig industry, though little is known about its population structure. We collected S. suis isolates from 144 farms in the years 2018-2022. All samples were taken from animals suffering from symptoms indicating possible S. suis infection. Serotyping revealed the presence of 23 different serotypes, and 18.94% were non-typable strains. The most common was S7 (14.96%), while other serotypes had frequencies of less than 10%. Sequence typing identified 56 different sequence types, including 31 newly assigned sequence types together with 41 new alleles in genes in the MLST schema. A large portion of isolates (25.70%) were of unknown sequence type. The most common sequence types were ST29 (14.77%) and ST28 (10.04%); the other sequence types had frequencies of less than 10%. In total, 100 different combinations of serotypes and sequence types were identified. Among them, S7ST29 was found in 72 isolates, representing 13.63% of all isolates, and was significantly associated with the central nervous system. Many other isolates of particular serotype and sequence type combinations were found in a few cases, and a number of isolates were non-typable.
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Affiliation(s)
| | - Bronislav Šimek
- State Veterinary Institute Jihlava, 586 01 Jihlava, Czech Republic
| | - Jan Gebauer
- Veterinary Research Institute, 621 00 Brno, Czech Republic
| | - Natálie Králová
- Veterinary Research Institute, 621 00 Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic
| | | | - Hana Plodková
- State Veterinary Institute Jihlava, 586 01 Jihlava, Czech Republic
| | - Tomáš Pecka
- State Veterinary Institute Jihlava, 586 01 Jihlava, Czech Republic
| | - Marek Brychta
- State Veterinary Institute Jihlava, 586 01 Jihlava, Czech Republic
| | - Marie Švejdová
- State Veterinary Institute Jihlava, 586 01 Jihlava, Czech Republic
| | | | | | - Ján Matiašovic
- Veterinary Research Institute, 621 00 Brno, Czech Republic
- Correspondence: ; Tel.: +420-533331317
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25
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Brossard Stoos KA, Ren J, Shields-Cutler RR, Sams KL, Caldwell S, Ho MB, Rivara G, Whistler CA, Jones SH, Wiedmann M, DeMent J, Getchell RG, Marquis H. Coastal water bacteriophages infect various sets of Vibrio parahaemolyticus sequence types. Front Microbiol 2022; 13:1041942. [PMID: 36601403 PMCID: PMC9807174 DOI: 10.3389/fmicb.2022.1041942] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 10/31/2022] [Indexed: 12/23/2022] Open
Abstract
Introduction Gastrointestinal illnesses associated with the consumption of shellfish contaminated with Vibrio parahaemolyticus have a negative impact on the shellfish industry due to recalls and loss of consumer confidence in products. This bacterial pathogen is very diverse and specific sequence types (STs), ST631 and ST36, have emerged as prevalent causes of Vibrio foodborne disease outbreaks in the US, though other STs have been implicated in sporadic cases. We investigated whether bacteriophages could be used as a proxy to monitor for the presence of distinct V. parahaemolyticus STs in coastal waters. Methods For this purpose, bacteriophages infecting V. parahaemolyticus were isolated from water samples collected on the Northeast Atlantic coast. The isolated phages were tested against a collection of 29 V. parahaemolyticus isolates representing 18 STs, including six clonal complexes (CC). Four distinct phages were identified based on their ability to infect different sets of V. parahaemolyticus isolates. Results and Discussion Overall, the 29 bacterial isolates segregated into one of eight patterns of susceptibility, ranging from resistance to all four phages to susceptibility to any number of phages. STs represented by more than one bacterial isolate segregated within the same pattern of susceptibility except for one V. parahaemolyticus ST. Other patterns of susceptibility included exclusively clinical isolates represented by distinct STs. Overall, this study suggests that phages populating coastal waters could be exploited to monitor for the presence of V. parahaemolyticus STs known to cause foodborne outbreaks.
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Affiliation(s)
- Kari A. Brossard Stoos
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, United States,Department of Health Promotion and Physical Education, Ithaca College, Ithaca, NY, United States,*Correspondence: Kari A. Brossard Stoos,
| | - Jennifer Ren
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, United States
| | | | - Kelly L. Sams
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, United States
| | - Shannon Caldwell
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, United States
| | - Marvin B. Ho
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, United States
| | - Gregg Rivara
- Cornell Cooperative Extension of Suffolk County, Southold, NY, United States
| | - Cheryl A. Whistler
- Northeast Center for Vibrio Disease and Ecology, University of New Hampshire, Durham, NH, United States,Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Stephen H. Jones
- Northeast Center for Vibrio Disease and Ecology, University of New Hampshire, Durham, NH, United States,Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, United States
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY, United States
| | - Jamie DeMent
- Florida Department of Health, Tallahassee, FL, United States
| | - Rodman G. Getchell
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, United States
| | - Hélène Marquis
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, United States
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Vanstokstraeten R., Crombé F., Piérard D., Castillo Moral A., Wybo I., De Geyter D., Janssen T., Caljon B., Demuyser T.. Molecular characterization of extraintestinal and diarrheagenic Escherichia coli blood isolates. Virulence 2022; 13:2032-2041. [PMID: 36397646 PMCID: PMC9704385 DOI: 10.1080/21505594.2022.2147735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pathogenic E. coli strains can be classified into two major groups, based on the presence of specific virulence factors: extraintestinal pathogenic E. coli (ExPEC) and diarrheagenic E. coli (DEC). Several case reports describe that DEC can cause bloodstream infections in some rare cases. This mainly concerns a few specific sequence types that express virulence factors from both ExPEC and DEC. In this study, we retrospectively analysed 234 E. coli blood isolates with whole genome sequencing (WGS). WGS was performed on an Illumina NovaSeq6000. Genotyping was performed using BioNumerics software. The presence of genes was determined with a minimum percentage sequence identity (ID) threshold of 95% and a minimum length for sequence coverage of 95%. Three of the 234 (1.28%) isolates were defined as DEC, 182 (77.78%) as ExPEC, and 49 (20.94%) did not carry pathotype-associated virulence genes. We identified 112 different virulence genes, 48 O-antigens, and 28 H-antigens 82 STs, among the 234 analyzed isolates. ST131 and ST88 were related to healthcare-associated infections. This study provides insight into the prevalence of virulence factors in a large set of E. coli blood isolates from the UZ Brussel. It illustrates high diversity in virulence profiles and highlights the potential of DEC to carry virulence factors associated with extraintestinal infections, making it possible for unusual pathotypes to invade and survive in the bloodstream causing bacteraemia. Diarrheagenic strains causing bacteremia are rare and presently underreported, but modern sequencing techniques will better underscore their importance.
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Affiliation(s)
- Vanstokstraeten R.
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis, Brussels, Belgium,CONTACT Vanstokstraeten R.
| | - Crombé F.
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis, Brussels, Belgium
| | - Piérard D.
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis, Brussels, Belgium
| | - Castillo Moral A.
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis, Brussels, Belgium
| | - Wybo I.
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis, Brussels, Belgium
| | - De Geyter D.
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis, Brussels, Belgium
| | - Janssen T.
- Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis, Brussels Interuniversity Genomics High Throughput core (BRIGHTcore) platform, Brussels, Belgium
| | - Caljon B.
- Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis, Brussels Interuniversity Genomics High Throughput core (BRIGHTcore) platform, Brussels, Belgium
| | - Demuyser T.
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis, Brussels, Belgium
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Fredriksson-Ahomaa M, Sauvala M, Kurittu P, Heljanko V, Heikinheimo A, Paulsen P. Characterisation of Listeria monocytogenes Isolates from Hunted Game and Game Meat from Finland. Foods 2022; 11:foods11223679. [PMID: 36429271 PMCID: PMC9689155 DOI: 10.3390/foods11223679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022] Open
Abstract
Listeria monocytogenes is an important foodborne zoonotic bacterium. It is a heterogeneous species that can be classified into lineages, serogroups, clonal complexes, and sequence types. Only scarce information exists on the properties of L. monocytogenes from game and game meat. We characterised 75 L. monocytogenes isolates from various game sources found in Finland between 2012 and 2020. The genetic diversity, presence of virulence and antimicrobial genes were studied with whole genome sequencing. Most (89%) of the isolates belonged to phylogenetic lineage (Lin) II and serogroup (SG) IIa. SGs IVb (8%) and IIb (3%) of Lin I were sporadically identified. In total, 18 clonal complexes and 21 sequence types (STs) were obtained. The most frequent STs were ST451 (21%), ST585 (12%) and ST37 (11%) found in different sample types between 2012 and 2020. We observed 10 clusters, formed by closely related isolates with 0-10 allelic differences. Most (79%) of the virulence genes were found in all of the L. monocytogenes isolates. Only fosX and lin were found out of 46 antimicrobial resistance genes. Our results demonstrate that potentially virulent and antimicrobial-sensitive L. monocytogenes isolates associated with human listeriosis are commonly found in hunted game and game meat in Finland.
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Affiliation(s)
- Maria Fredriksson-Ahomaa
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, 00014 Helsinki, Finland
- Correspondence:
| | - Mikaela Sauvala
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Paula Kurittu
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Viivi Heljanko
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Annamari Heikinheimo
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, 00014 Helsinki, Finland
- Microbiology Unit, Finnish Food Authority, 60100 Seinäjoki, Finland
| | - Peter Paulsen
- Unit of Food Hygiene and Technology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, 1210 Vienna, Austria
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Kerdsin A. Human Streptococcus suis Infections in Thailand: Epidemiology, Clinical Features, Genotypes, and Susceptibility. Trop Med Infect Dis 2022; 7:359. [PMID: 36355901 PMCID: PMC9695567 DOI: 10.3390/tropicalmed7110359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 10/29/2023] Open
Abstract
Streptococcus suis is a zoonotic pathogen causing substantial economic losses to the pig industry, as well as being a human health burden due to infections worldwide, especially in Southeast Asia. In Thailand, there was high cumulative incidence in humans during 1987-2021, mostly in males. At least five large outbreaks have been documented after the largest outbreak in China in 2005, which was related to the consumption of raw pork or dishes containing pig's blood. The major clinical features are sepsis or meningitis, with hearing loss a major complication of S. suis disease. Thai human S. suis isolates have shown diversity in serotypes and sequence types (STs), with serotype 2 and STs 1 and 104 being major genotypes. β-Lactam antibiotics can be used in empirical treatment for human S. suis infections; however, intermediate resistance to penicillin has been reported. Reducing S. suis incidence in Thailand requires a multidimensional approach, with combined efforts from the government and public health sectors through policy, regulations, education, and active surveillance.
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Affiliation(s)
- Anusak Kerdsin
- Faculty of Public Health, Kasetsart University, Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon 47000, Thailand
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Hitchcock M, Xu J. Analyses of the Global Multilocus Genotypes of the Human Pathogenic Yeast Cryptococcus neoformans Species Complex. Genes (Basel) 2022; 13:2045. [PMID: 36360282 PMCID: PMC9691084 DOI: 10.3390/genes13112045] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 12/18/2023] Open
Abstract
Cryptococcus neoformans species complex (CNSC) is a globally distributed human opportunistic yeast pathogen consisting of five major molecular types (VNI, VNII, VNB, VNIII and VNIV) belonging to two species, C. neoformans (VNI, VNII and VNB, collectively called serotype A) and C. deneoformans (VNIV, commonly called serotype D), and their hybrids (VNIII, serotype AD). Over the years, many studies have analyzed the geographical distribution and genetic diversity of CNSC. However, the global population structure and mode of reproduction remain incompletely described. In this study, we analyze the published multilocus sequence data at seven loci for CNSC. The combined sequences at the seven loci identified a total of 657 multilocus sequence types (STs), including 296 STs with known geographic information, representing 4200 non-redundant isolates from 31 countries and four continents. Among the 296 STs, 78 and 52 were shared among countries and continents, respectively, representing 3643 of the 4200 isolates. Except for the clone-corrected serotype D sample among countries, our analysis of the molecular variance of the 4200 isolates revealed significant genetic differentiations among countries and continents in populations of CNSC, serotype A, and serotype D. Phylogenetic analyses of the concatenated sequences of all 657 STs revealed several large clusters corresponding to the major molecular types. However, several rare but distinct STs were also found, representing potentially novel molecular types and/or hybrids of existing molecular types. Phylogenetic incompatibility analyses revealed evidence for recombination within all four major molecular types-VNI, VNII, VNIV and VNB-as well as within two VNB subclades, VNBI and VNBII, and two ST clusters around the most common STs, ST5 and ST93. However, linkage disequilibrium analyses rejected the hypothesis of random recombination across most samples. Together, our results suggest evidence for historical differentiation, frequent recent gene flow, clonal expansion and recombination within and between lineages of the global CNSC population.
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Affiliation(s)
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
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Koh Y, Bae Y, Lee YS, Kang DH, Kim SH. Prevalence and Characteristics of Salmonella spp. Isolated from Raw Chicken Meat in the Republic of Korea. J Microbiol Biotechnol 2022; 32:1307-1314. [PMID: 36198666 PMCID: PMC9668092 DOI: 10.4014/jmb.2207.07031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/01/2022] [Accepted: 09/05/2022] [Indexed: 12/15/2022]
Abstract
In this study, we sought to investigate the various characteristics of Salmonella spp. isolated from raw chicken meats available in Korean markets. The data collected, such as food source of isolation, sampling information, serotype, virulence, and genetic profile including sequence type, were registered in the database for further comparative analysis of the strains isolated from the traceback investigation samples. To characterize serotype, virulence and gene sequences, we examined 113 domestically distributed chicken meat samples for contamination with Salmonella spp. Phylogenetic analysis was conducted on 24 strains (21.2%) of Salmonella isolated from 113 commercially available chicken meats and by-products, using pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Serotyping of the isolated Salmonella spp. revealed S. Enteritidis in 11 strains (45.8%), S. Virchow in 6 strains (25%), S. Montevideo in 2 strains (8.3%), S. Bsilla in 2 strains (8.3%), S. Bareilly in 1 strain (4.2%), S. Dessau in 1 strain (4.2%), and S. Albany in 1 strain (4.2%). The genetic correlation indicated that 24 isolated strains were classified into 18 clusters with a genetic similarity of 64.4-100% between them. Eleven isolated S. Enteritidis strains were classified into 9 genotypes with a sequence identity of 74.4%, whereas the most distantly related S. Virchow was divided into five genotypes with 85.9% identity. Here, the MLST analysis indicated that the major Sequence Type (ST) of the Salmonella spp. isolated from domestic chicken sold in Chungcheong Province belongs to the ST 11 and 16, which differs from the genotype of Salmonella isolated from imported chicken. The differential sequence characteristics can be a genetic marker for identifying causative bacteria for epidemiological investigations of food poisoning.
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Affiliation(s)
- Youngho Koh
- Food Microbiology Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea,Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Research Institute for Agricultural and Life Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Yunyoung Bae
- Food Microbiology Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea
| | - Yu-Si Lee
- Food Microbiology Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea
| | - Dong-Hyun Kang
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Research Institute for Agricultural and Life Science, Seoul National University, Seoul 08826, Republic of Korea,
D.H. Kang Phone: +82-880-2697 E-mail:
| | - Soon Han Kim
- Food Microbiology Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea,Corresponding authorsS. H. Kim Phone: +82-43-719-4303 Fax: +82-43-719-4303 E-mail:
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Mafuna T, Matle I, Magwedere K, Pierneef RE, Reva ON. Comparative Genomics of Listeria Species Recovered from Meat and Food Processing Facilities. Microbiol Spectr 2022; 10:e0118922. [PMID: 36066257 PMCID: PMC9604131 DOI: 10.1128/spectrum.01189-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 08/12/2022] [Indexed: 12/30/2022] Open
Abstract
Listeria species (spp.) are contaminants that can survive in food, on equipment, and on food processing premises if appropriate hygiene measures are not used. Homologous stress tolerance genes, virulence gene clusters such as the prfA cluster, and clusters of internalin genes that contribute to the pathogenic potential of the strains can be carried by both pathogenic and nonpathogenic Listeria spp. To enhance understanding of the genome evolution of virulence and virulence-associated properties, a comparative genome approach was used to analyze 41 genome sequences belonging to L. innocua and L. welshimeri isolated from food and food processing facilities. Genetic determinants responsible for disinfectant and stress tolerance were identified, including the efflux cassette bcrABC and Tn6188_qac_1 disinfectant resistance determinant, and stress survival islets. These disinfectant-resistant genes were more frequently found in L. innocua (12%) than in L. welshimeri (2%). Several isolates representing the presumed nonpathogenic L. innocua still carried virulence-associated genes, including LGI2, LGI3, LIPI-3, and LIPI-4 which were absent in all L. welshimeri isolates. The mobile genetic elements identified were plasmids (pLGUG1 and J1776) and prophages (PHAGE_Lister_vB_LmoS_188, PHAGE_Lister_LP_030_3, PHAGE_Lister_A118, PHAGE_Lister_B054, and PHAGE_Lister_vB_LmoS_293). The results suggest that the presumed nonpathogenic isolates especially L. innocua can carry genes relevant to the strain's virulence and stress tolerance in the food and food processing facilities. IMPORTANCE This study provides genomic insights into the recently expanded genus in order to gain valuable information about the evolution of the virulence and stress tolerance properties of the genus Listeria and the distribution of these genetic elements pertinent to the pathogenic potential across Listeria spp. and clonal lineages in South Africa (SA).
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Affiliation(s)
- T. Mafuna
- Department of Biochemistry, University of Johannesburg, Auckland Park, South Africa
- Biotechnology Platform, Agricultural Research Council, Onderstepoort, South Africa
| | - I. Matle
- Bacteriology Division, Agricultural Research Council, Onderstepoort Veterinary Research, Onderstepoort, South Africa
| | - K. Magwedere
- Directorate of Veterinary Public Health, Department of Agriculture, Land Reform and Rural Development, Pretoria, South Africa
| | - R. E. Pierneef
- Biotechnology Platform, Agricultural Research Council, Onderstepoort, South Africa
| | - O. N. Reva
- Centre for Bioinformatics and Computational Biology, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
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Lindstedt K, Buczek D, Pedersen T, Hjerde E, Raffelsberger N, Suzuki Y, Brisse S, Holt K, Samuelsen Ø, Sundsfjord A. Detection of Klebsiella pneumoniae human gut carriage: a comparison of culture, qPCR, and whole metagenomic sequencing methods. Gut Microbes 2022; 14:2118500. [PMID: 36045603 PMCID: PMC9450895 DOI: 10.1080/19490976.2022.2118500] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Klebsiella pneumoniae is an important opportunistic healthcare-associated pathogen and major contributor to the global spread of antimicrobial resistance. Gastrointestinal colonization with K. pneumoniae is a major predisposing risk factor for infection and forms an important hub for the dispersal of resistance. Current culture-based detection methods are time consuming, give limited intra-sample abundance and strain diversity information, and have uncertain sensitivity. Here we investigated the presence and abundance of K. pneumoniae at the species and strain level within fecal samples from 103 community-based adults by qPCR and whole metagenomic sequencing (WMS) compared to culture-based detection. qPCR demonstrated the highest sensitivity, detecting K. pneumoniae in 61.2% and 75.8% of direct-fecal and culture-enriched sweep samples, respectively, including 52/52 culture-positive samples. WMS displayed lower sensitivity, detecting K. pneumoniae in 71.2% of culture-positive fecal samples at a 0.01% abundance cutoff, and was inclined to false positives in proportion to the relative abundance of other Enterobacterales present. qPCR accurately quantified K. pneumoniae to 16 genome copies/reaction while WMS could estimate relative abundance to at least 0.01%. Quantification by both methods correlated strongly with each other (Spearman's rho = 0.91). WMS also supported accurate intra-sample K. pneumoniae sequence type (ST)-level diversity detection from fecal microbiomes to 0.1% relative abundance, agreeing with the culture-based detected ST in 16/19 samples. Our results show that qPCR and WMS are sensitive and reliable tools for detection, quantification, and strain analysis of K. pneumoniae from fecal samples with potential to support infection control and enhance insights in K. pneumoniae gastrointestinal ecology.
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Affiliation(s)
- Kenneth Lindstedt
- Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway,CONTACT Kenneth Lindstedt
| | - Dorota Buczek
- Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway
| | - Torunn Pedersen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Erik Hjerde
- Department of Chemistry, UiT the Arctic University of Norway, Tromsø, Norway
| | - Niclas Raffelsberger
- Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway,Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, The University of Tokyo, Tokyo, Japan
| | - Sylvain Brisse
- Biodiversity and Epidemiology of Bacterial Pathogens Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | - Kathryn Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia,Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Ørjan Samuelsen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway,Department of Pharmacy, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway
| | - Arnfinn Sundsfjord
- Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway,Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway,Arnfinn Sundsfjord Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, 9038, Norway
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Zhang Z, Dong Y, Xiang F, Wang Y, Hou Q, Ni H, Cai W, Liu W, Yang S, Guo Z. Analysis of bacterial diversity and genetic evolution of Lacticaseibacillus paracasei isolates in fermentation pit mud. J Appl Microbiol 2022; 133:1821-1831. [PMID: 35802775 DOI: 10.1111/jam.15672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 04/13/2022] [Accepted: 06/14/2022] [Indexed: 11/30/2022]
Abstract
AIMS Since little is known about the genetic diversity of lactic acid bacteria (LAB) isolates from the fermentation pit mud (FPM), we sought to evaluate the bacterial structure, identify the LAB isolates and investigate the genotype and genetic diversity of the LAB isolates. METHODS AND RESULTS Using high-throughput MiSeq sequencing, we identified seven dominant bacterial genera in FPM. Lactobacillus had the highest abundance. We isolated 55 LAB strains. These isolates were all identified as Lacticaseibacillus paracasei. Using an extant multilocus sequence typing (MLST) scheme, isolates were assigned to 18 sequence types (STs) and three clonal complexes. ST1, the largest group, mainly comprised FPM isolates. Niche-specific ST2 to ST18 only contained FPM isolates. Isolates could be divided into four lineages, with most assigned to Lineage 1. Only one FPM isolate was classified as L. paracasei subsp. paracasei. Other isolates could not be classified at the subspecies level using the seven MLST loci. CONCLUSIONS Lactobacilli account for a high proportion of bacteria in pit mud. Based on the traditional culture method, L. paracasei was the dominant species, and these isolates exhibit a high ethanol tolerance, high intraspecific diversity and specific genetic profiles. SIGNIFICANCE AND IMPACT OF THE STUDY The study described the characterization of FPM bacterial diversity, giving an insight into the genetic diversity of L. paracasei strains present in FPM.
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Affiliation(s)
- Zhendong Zhang
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, People's Republic of China
| | - Yun Dong
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, People's Republic of China
| | - Fanshu Xiang
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, People's Republic of China
| | - Yurong Wang
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, People's Republic of China
| | - Qiangchuan Hou
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, People's Republic of China
| | - Hui Ni
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, People's Republic of China.,School of Food Science, Shihezi University, Shihezi, Xinjiang Autonomous Region, People's Republic of China
| | - Wenchao Cai
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, People's Republic of China.,School of Food Science, Shihezi University, Shihezi, Xinjiang Autonomous Region, People's Republic of China
| | - Wenhui Liu
- Hubei Guxiangyang Liquor Industry Co., Ltd., Xiangyang, People's Republic of China
| | - Shaoyong Yang
- Hubei Guxiangyang Liquor Industry Co., Ltd., Xiangyang, People's Republic of China
| | - Zhuang Guo
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, People's Republic of China
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Sasaki Y, Nozawa-Takeda T, Yonemitsu K, Asai T, Asakura H, Nagai H. Characterization of Campylobacter jejuni in large-billed crows (Corvus macrorhynchos) in Tochigi prefecture, Japan. J Vet Med Sci 2022; 84:1029-1033. [PMID: 35650120 PMCID: PMC9353090 DOI: 10.1292/jvms.22-0055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
As free-living crows are a potential source of Campylobacter infections in broilers and cattle, we characterized Campylobacter spp. isolated from crows
using multilocus sequence typing and antimicrobial susceptibility testing. We obtained 82 samples from 27 birds captured at seven different times using a trap set in Tochigi prefecture,
Japan. Campylobacter jejuni was isolated from 55 (67.1%) of the 82 samples and classified into 29 sequence types, of which 21 were novel. Tetracycline and streptomycin
resistance rates were 18.2% and 3.6%, respectively. These results show that most types of C. jejuni infecting crows differ from those isolated from humans, broilers, and
cattle. Thus, the importance of free-living crows as reservoirs of Campylobacter infections in broilers and cattle may be limited.
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Affiliation(s)
- Yoshimasa Sasaki
- Division of Biomedical Food Research, National Institute of Health Sciences.,Department of Applied Veterinary Science, the United Graduate School of Veterinary Science, Gifu University
| | - Tsutomu Nozawa-Takeda
- Department of Agriculture, Utsunomiya University.,Tamanoura Area Future Association, Goto City Tamanoura Branch
| | | | - Tetsuo Asai
- Department of Applied Veterinary Science, the United Graduate School of Veterinary Science, Gifu University
| | - Hiroshi Asakura
- Division of Biomedical Food Research, National Institute of Health Sciences.,Department of Applied Veterinary Science, the United Graduate School of Veterinary Science, Gifu University
| | - Hidetaka Nagai
- National Veterinary Assay Laboratory, Ministry of Agriculture, Forestry and Fisheries
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Bocharova YA, Savinova TA, Lyamin AV, Kondratenko OV, Polikarpova SV, Zhilina SV, Fedorova NI, Semykin SY, Chaplin AV, Korostin DO, Mayansky NA, Chebotar IV. Characteristics of Stenotrophomonas maltophilia isolates from cystic fibrosis patients in Russia. Klin Lab Diagn 2022; 67:315-320. [PMID: 35613352 DOI: 10.51620/0869-2084-2022-67-5-315-320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Stenotrophomonas maltophilia is a common opportunistic microorganism and an important respiratory pathogen in cystic fibrosis (CF). The aim of this study was to determine antimicrobial resistance phenotypes, sequence-types (ST) and genetic determinants of antibiotic resistance in S. maltophilia strains recovered from CF patients in Russia. S. maltophilia isolates recovered from 170 CF patients were analyzed. Minimum inhibitory concentrations of antibacterial agents were determined using Sensititre Gram Negative GNX2F plates and the results were interpreted according to Clinical and Laboratory Standards Institute (CLSI) criteria. Whole-genome sequencing (WGS) was performed on MGISEQ-2000 platform. SPAdes software, Galaxy, ResFinder, Integrall and PubMLST were used for analysis of WGS data. S. maltophilia strains were identified from 24/170 (14%) CF patients. In total, 25 isolates were detected, two strains were isolated from the same patient. The isolates belonged to 17 different STs, including 5 new STs; ST4 was the most prevalent ST. Resistance to ceftazidime was observed in 60% of strains, to ticarcillin-clavulanate - in 32%, to levofloxacin - in 24%, to trimethoprim/sulfamethoxazole - in 12% of strains. All isolates were susceptible to minocycline. All ST4 isolates were resistant or intermediate to ceftazidime and ticarcillin-clavulanate. In two isolates, the sul1 gene was detected. In one isolate, sul1 was part of a class 1 integron. The detected integron also contained the blaGES-7 and aac(6')-Ib-cr genes. The ST4 sequence-type was the most prevalent ST among S. maltophilia strains recovered from CF patients in Russia. Antibiotic resistance genes, including sul1, blaGES-7, aac(6')-Ib-cr, were detected in single strains.
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Affiliation(s)
| | - T A Savinova
- Pirogov Russian National Research Medical University
| | | | | | | | | | - N I Fedorova
- Pirogov Russian National Research Medical University
| | - S Yu Semykin
- Pirogov Russian National Research Medical University
| | - A V Chaplin
- Pirogov Russian National Research Medical University
| | - D O Korostin
- Pirogov Russian National Research Medical University
| | - N A Mayansky
- Pirogov Russian National Research Medical University
| | - I V Chebotar
- Pirogov Russian National Research Medical University
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36
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Aung KT, Khor WC, Ong KH, Tan WL, Wong ZN, Oh JQ, Wong WK, Tan BZY, Maiwald M, Tee NWS, Barkham T, Koh TH, Dalsgaard A, Chen SL, Schlundt J, Ng LC. Characterisation of Salmonella Enteritidis ST11 and ST1925 Associated with Human Intestinal and Extra-Intestinal Infections in Singapore. Int J Environ Res Public Health 2022; 19:5671. [PMID: 35565065 DOI: 10.3390/ijerph19095671] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/01/2022] [Accepted: 05/03/2022] [Indexed: 12/04/2022]
Abstract
Salmonella Enteritidis is a major foodborne pathogen worldwide. In this study, a total of 276 S. enteritidis isolates, collected between 2016 and 2017 from human, food and farm/slaughterhouse samples, were studied to enhance the understanding of the epidemiology of human salmonellosis in Singapore. Results showed all 276 isolates belonged either to ST1925 (70.3%) or ST11 (29.7%), with ST11 being significantly more frequent in extra-intestinal isolates and chicken isolates. Food isolates, most of which were from poultry, showed the highest prevalence of resistance (33–37%) against beta-lactams or beta-lactams/beta-lactamase inhibitor combination (ampicillin, piperacillin and ampicillin/sulbactam). The analysis showed the detection of genes associated with resistance to aminoglycoside genes (99.6%), tetracycline (55.1%), and beta-lactams (14.9%) of all isolates. Nine types of plasmids were found in 266 isolates; the most common incompatibility group profiles were IncFIB(S)-IncFII(S)-IncX1 (72.2%) and IncFIB(S)-IncFII(S) (15.8%). Most plasmid harbouring isolates from chicken (63.6%, 14/22) and from human (73.8%, 175/237) shared the same plasmid profile (IncFIB(S)-IncFII(S)-IncX1). SNP analysis showed clustering of several isolates from poultry food products and human isolates, suggesting phylogenetic relatedness among these isolates. Lastly, this study provides important epidemiological insights on the application of phenotypic and next-generation sequencing (NGS) tools for improved food safety and public health surveillance and outbreak investigation of S.enteritidis.
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Takeuchi D, Kerdsin A, Akeda Y, Sugawara Y, Sakamoto N, Matsumoto Y, Motooka D, Ishihara T, Nishi I, Laolerd W, Santanirand P, Yamamoto N, Tomono K, Hamada S. Nationwide surveillance in Thailand revealed genotype-dependent dissemination of carbapenem-resistant Enterobacterales. Microb Genom 2022; 8. [PMID: 35438076 PMCID: PMC9453063 DOI: 10.1099/mgen.0.000797] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Carbapenem-resistant
Enterobacterales
(CRE) are a serious public health threat because of their rapid dissemination. To determine the epidemiological and genetic characteristics of CRE infections in Thailand, we performed whole-genome sequencing of 577 carbapenem-resistant
Klebsiella pneumoniae
isolates and 170 carbapenem-resistant
Escherichia coli
isolates from hospitals across the nation. The four most prevalent carbapenemase genes harboured by these bacteria were bla
NDM-1, bla
NDM-5, bla
OXA-181 and bla
OXA-232. The gene bla
NDM-1 was identified in diverse sequence types. The gene bla
NDM-5 was identified almost exclusively in
E. coli
. The genes bla
OXA-181, bla
OXA-232, and co-carriage of bla
NDM-1 and bla
OXA-232 were found in specific sequence types from certain provinces. Replicon typing revealed the diverse backbones of bla
NDM-1- and bla
NDM-5-harbouring plasmids and successful expansion of bla
NDM-1-harbouring IncN2-type plasmids. Core-genome single-nucleotide polymorphism analysis suggested that bla
OXA-181-, bla
OXA-232-, bla
NDM-5-, and co-carriage of bla
NDM-1 and bla
OXA-232-associated sub-clonal lineages have recently predominated in the provinces from where these isolates were isolated. Thus, we demonstrate genotype-dependent dissemination of CRE in Thailand, which is helpful for establishing infection-control strategies in CRE-endemic areas.
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Affiliation(s)
- Dan Takeuchi
- Japan-Thailand Research Collaboration Center, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Anusak Kerdsin
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Yukihiro Akeda
- Japan-Thailand Research Collaboration Center, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Yo Sugawara
- Japan-Thailand Research Collaboration Center, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Noriko Sakamoto
- Japan-Thailand Research Collaboration Center, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Yuki Matsumoto
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Daisuke Motooka
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Takuma Ishihara
- Innovative and Clinical Research Promotion Center, Gifu University Hospital, Gifu, Japan
| | - Isao Nishi
- Division of Infection Control and Prevention, Osaka University Hospital, Suita, Japan
| | - Warawut Laolerd
- Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Pitak Santanirand
- Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Norihisa Yamamoto
- Japan-Thailand Research Collaboration Center, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Kazunori Tomono
- Division of Infection Control and Prevention, Osaka University Hospital, Suita, Japan
| | - Shigeyuki Hamada
- Japan-Thailand Research Collaboration Center, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
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Kerdsin A, Segura M, Fittipaldi N, Gottschalk M. Sociocultural Factors Influencing Human Streptococcus suis Disease in Southeast Asia. Foods 2022; 11:foods11091190. [PMID: 35563913 PMCID: PMC9102869 DOI: 10.3390/foods11091190] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 04/16/2022] [Accepted: 04/19/2022] [Indexed: 12/29/2022] Open
Abstract
The public health systems of Southeast Asian countries are financially challenged by a comparatively higher incidence of human S. suis infections than other geographical areas. Efforts to improve practices in production settings, including improved meat inspection regulations, prevention of the slaughtering of non-healthy pigs, and enhanced hygiene practices at processing facilities, along with improvements in the pork supply chain, all appear promising for reducing food cross-contamination with S. suis. However, opportunities for intervention at the societal level are also needed to effect changes, as population behaviors such as the consumption of raw pork, blood, and offal products are important contributors to the increased incidence of human S. suis disease in Southeast Asia. A plethora of factors are associated with the consumption of these high-risk dishes, including traditional culture and knowledge, shared beliefs, socio-economic level, and personal attitudes associated with gender and/or marital status. Education and intervention in behavioral attitudes that are sensible to cultural practices and traditions may provide additional means to reduce the burden of S. suis human disease in Southeast Asia.
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Affiliation(s)
- Anusak Kerdsin
- Faculty of Public Health, Kasetsart University, Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon 47000, Thailand
- Correspondence: ; Tel.: +66-42-725-023
| | - Mariela Segura
- Research Group on Infectious Diseases in Production Animals (GREMIP) and Swine and Poultry Infectious Diseases Research Center (CRIPA), Faculty of Veterinary Medicine, University of Montreal, St-Hyacinthe, QC J2S 2M2, Canada; (M.S.); (N.F.); (M.G.)
| | - Nahuel Fittipaldi
- Research Group on Infectious Diseases in Production Animals (GREMIP) and Swine and Poultry Infectious Diseases Research Center (CRIPA), Faculty of Veterinary Medicine, University of Montreal, St-Hyacinthe, QC J2S 2M2, Canada; (M.S.); (N.F.); (M.G.)
| | - Marcelo Gottschalk
- Research Group on Infectious Diseases in Production Animals (GREMIP) and Swine and Poultry Infectious Diseases Research Center (CRIPA), Faculty of Veterinary Medicine, University of Montreal, St-Hyacinthe, QC J2S 2M2, Canada; (M.S.); (N.F.); (M.G.)
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Takahashi H, Morita M, Kamiya H, Nakamura-Miwa H, Shimuta K, Ohnishi M. Genetic characterization of clonal complex sequence type 2057 (cc2057) serogroup B Neisseria meningitidis strains unique to Japan and identification of a capsular-switched serogroup Y isolate cc2057. J Med Microbiol 2022; 71. [PMID: 35238737 DOI: 10.1099/jmm.0.001504] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. Only approximately 40 cases of invasive meningococcal diseases are reported annually in Japan, and the dominant strains are serogroup Y meningococci (MenY) followed by serogroup B meningococci (MenB). Within the last 10 years, Neisseria meningitidis strains belonging to clonal complex (cc)2057 have become dominant among Japanese MenB and have not been identified in countries other than Japan.Hypothesis/Gap Statement. The uniqueness of cc2057 N. meningitidis strains was considered to be epidemiologically of importance, and some genetic features could be hidden in the genome of cc2057 meningococci.Method. We investigated 22 cc2057 MenB and one cc2057 MenY using whole genome sequencing (WGS) and also predicted the potential coverage of 4CMenB and bivalent rLP2086 vaccines in silico.Results. cc2057 N. meningitidis strains were phylogenetically assigned to two clades. Three hypothetical genes homologous to those in Neisseria lactamica and sequences related to a new CRISPR Cas9 system were found only in the genome of cc2057 strains. Moreover, one cc2057 MenY strain was presumed to be capsular-switched at the capsule synthesis (cps) locus. The potential coverage of 4CMenB and rLP2086 for cc2057 MenB strains was estimated to be very low.Conclusion. To the best of our knowledge, this is the first study to provide genetic insights from epidemiologically unique N. meningitidis cc2057 strains isolated only in Japan, an island country.
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Affiliation(s)
- Hideyuki Takahashi
- Department of Bacteriology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Masatomo Morita
- Department of Bacteriology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hajime Kamiya
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Haruna Nakamura-Miwa
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Ken Shimuta
- Department of Bacteriology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Ohnishi
- Department of Bacteriology, National Institute of Infectious Diseases, Tokyo, Japan
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40
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Feodorova VA, Saltykov YV, Kolosova AA, Rubanik LV, Poleshchuk NN, Motin VL. Emergence of Novel Chlamydia trachomatis Sequence Types among Chlamydia Patients in the Republic of Belarus. Microorganisms 2022; 10:478. [PMID: 35208932 DOI: 10.3390/microorganisms10020478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/15/2022] [Accepted: 02/18/2022] [Indexed: 11/17/2022] Open
Abstract
Chlamydia trachomatis (CT) is a major cause of sexually transmitted diseases worldwide. The multilocus sequence typing (MLST) of clinical samples from random heterosexual chlamydia patients who were either asymptomatic or reported clinical manifestations of genital chlamydiosis (n = 63) in each of the seven major regions of the Republic of Belarus in 2017–2018 revealed 12 different CT sequence types (STs). We found seven known STs, ST4, ST6, ST9, ST13, ST38, ST95 and ST110, and five novel variants, namely ST271–ST275, which have not been detected elsewhere thus far. The ST4 variant was predominant (27/63, 42.9%) and detected in six out of seven regions. The two most common STs, ST9 and ST13, were regularly seen in four out of seven regions. In contrast, the remaining STs, ST6, ST38, ST95, ST110, and novel STs271-275, surfaced randomly in different parts of the country. The emergence of novel STs was registered in two regions, namely Minsk (ST271 and ST275) and Brest (ST271, ST272, ST273, and ST274). All the STs of detected CT strains were clustered into two Groups, I and III, which are characteristic of CT urogenital strains. No STs typical for Group II, specific to the LGV strains, were revealed. Our study contributes to better understanding the genetic diversity and molecular evolution of CT, one of the most important pathogens in public health worldwide.
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41
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Guillemot J, Ginevra C, Allam C, Kay E, Gilbert C, Doublet P, Jarraud S, Chapalain A. TNF-α response in macrophages depends on clinical Legionella pneumophila isolates genotypes. Virulence 2022; 13:160-173. [PMID: 35030980 PMCID: PMC8765069 DOI: 10.1080/21505594.2021.2022861] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Legionnaires' Disease (LD) is a severe pneumonia mainly caused in Europe by Legionella pneumophila serogroup 1 (Lp1). Sequence-based typing methods reveal that some sequence types (ST) are overrepresented in clinical samples such as ST1 and ST47, suggesting that some strains are more fit for infection than others. In the present study, a collection of 108 Lp1 clinical isolates were used to evaluate the strain-dependent immune responses from human macrophages. Clinical Lp1 isolates induced differential TNFα secretion from macrophages. ST1 isolates induced a significantly higher TNF-α secretion than non-ST1, whereas ST47 isolates induced a significantly lower TNF-α secretion than non-ST47 isolates. ST1 isolates induced a significantly higher cell death than ST47 isolates evaluated by lactate dehydrogenase activity (cytotoxicity) and caspase-3 activity (apoptosis). Treatment of macrophages with anti-TNF-α antibodies significantly reduced the cell death in macrophages infected with ST1 or ST47 strains. The TNF-α secretion was neither explained by a differential bacterial replication nor by the number or type (bystander or infected) of TNF-α producing cells following infection but by a differential response from macrophages. The Paris ST1 reference strain elicited a significantly higher TNF-α gene transcription and a higher induction of NF-κB signaling pathway than the Lorraine ST47 reference strain.Clinical Lp1 isolates induce a diverse immune response and cell death, which could be related to the genotype. The two predominant sequence-types ST1 and ST47 trigger opposite inflammatory response that could be related to the host susceptibility.
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Affiliation(s)
- Johann Guillemot
- Ciri, Centre International de Recherche En Infectiologie, Équipe Pathogenèse Des Légionelles, Université Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, Lyon, France
| | - Christophe Ginevra
- Ciri, Centre International de Recherche En Infectiologie, Équipe Pathogenèse Des Légionelles, Université Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, Lyon, France.,Hospices Civils de Lyon, Institut Des Agents Infectieux, Centre National de Référence Des Légionelles, Lyon, France
| | - Camille Allam
- Ciri, Centre International de Recherche En Infectiologie, Équipe Pathogenèse Des Légionelles, Université Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, Lyon, France.,Hospices Civils de Lyon, Institut Des Agents Infectieux, Centre National de Référence Des Légionelles, Lyon, France
| | - Elisabeth Kay
- Ciri, Centre International de Recherche En Infectiologie, Équipe Pathogenèse Des Légionelles, Université Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, Lyon, France
| | - Christophe Gilbert
- Ciri, Centre International de Recherche En Infectiologie, Équipe Pathogenèse Des Légionelles, Université Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, Lyon, France
| | - Patricia Doublet
- Ciri, Centre International de Recherche En Infectiologie, Équipe Pathogenèse Des Légionelles, Université Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, Lyon, France
| | - Sophie Jarraud
- Ciri, Centre International de Recherche En Infectiologie, Équipe Pathogenèse Des Légionelles, Université Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, Lyon, France.,Hospices Civils de Lyon, Institut Des Agents Infectieux, Centre National de Référence Des Légionelles, Lyon, France
| | - Annelise Chapalain
- Ciri, Centre International de Recherche En Infectiologie, Équipe Pathogenèse Des Légionelles, Université Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, Lyon, France
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Kerdsin A, Hatrongjit R, Wongsurawat T, Jenjaroenpun P, Chopjitt P, Boueroy P, Fittipaldi N, Zheng H, Gottschalk M. Genomic Characterization of Streptococcus suis Serotype 24 Clonal Complex 221/234 From Human Patients. Front Microbiol 2022; 12:812436. [PMID: 35003043 PMCID: PMC8733411 DOI: 10.3389/fmicb.2021.812436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 12/06/2021] [Indexed: 12/26/2022] Open
Abstract
Streptococcus suis is a zoonotic pathogen that causes invasive infections in humans and pigs. Although S. suis serotype 2 is prevalent among patient and swine infections, other serotypes are occasionally detected in humans. Of these, serotype 24 clonal complex (CC) 221/234 are recognized as emerging clones of human infection. Genomic exploration of three S. suis serotype 24 CC221/234 strains revealed antimicrobial resistance genes, pathotyping, virulence-associated gene (VAG) profiles, minimum core genome (MCG) typing, and comparison of the genomes. Based on these analyzes, all three serotype 24 strains were MCG7-3 and should be classified in the intermediate/weakly virulent (I/WV) group. All selected serotype 24 strains were susceptible to several antibiotics including β-lactam, fluoroquinolone, and chloramphenicol. Resistance to tetracycline, macrolide, and clindamycin was observed and attributed to the genes tet(O) and erm(B). Genomic comparison revealed the strains S12X, LSS66, LS0L, LS0E, 92–4,172, and IMT40201 that had phylogenetic affinity with serotype 24 CC221/234. Analysis of 80 virulence-associated genes (VAG) showed that all three serotype 24 strains lacked 24 genes consisting of adhesin P, epf, hyl, ihk, irr, mrp, nadR, neuB, NisK/R, ofs, permease (SSU0835), rgg, revS, salK/R, sao, sly, spyM3_0908, srtBCD, srtF, srtG, SSU05_0473, virA, virB4, and virD4. Eleven specific sequences were identified in the 3 serotype 24 genomes that differed from the genomes of the representative strains of epidemic (E; SC84), highly virulent (HV; P1/7), I/WV (89–1,591), and avirulent (T15 and 05HAS68).
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Affiliation(s)
- Anusak Kerdsin
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Rujirat Hatrongjit
- Department of General Sciences, Faculty of Science and Engineering, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Thidathip Wongsurawat
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Piroon Jenjaroenpun
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Peechanika Chopjitt
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Parichart Boueroy
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Nahuel Fittipaldi
- Research Group on Infectious Diseases in Production Animals (GREMIP), Faculty of Veterinary Medicine, University of Montreal, Quebec, QC, Canada
| | - Han Zheng
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Marcelo Gottschalk
- Research Group on Infectious Diseases in Production Animals (GREMIP), Faculty of Veterinary Medicine, University of Montreal, Quebec, QC, Canada
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Fursova AD, Fursov MV, Astashkin EI, Novikova TS, Fedyukina GN, Kislichkina AA, Alexandrova IA, Ershova ON, Dyatlov IA, Fursova NK. Early Response of Antimicrobial Resistance and Virulence Genes Expression in Classical, Hypervirulent, and Hybrid hvKp-MDR Klebsiella pneumoniae on Antimicrobial Stress. Antibiotics (Basel) 2021; 11:7. [PMID: 35052884 DOI: 10.3390/antibiotics11010007] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 12/16/2022] Open
Abstract
Klebsiella pneumoniae is an increasingly important hospital pathogen. Classical K. pneumoniae (cKp) and hypervirulent K. pneumoniae (hvKp) are two distinct evolutionary genetic lines. The recently ongoing evolution of K. pneumoniae resulted in the generation of hybrid hvKP-MDR strains. K. pneumoniae distinct isolates (n = 70) belonged to 20 sequence types with the prevalence of ST395 (27.1%), ST23 (18.6%), ST147 (15.7%), and ST86 (7.1%), and 17 capsular types with the predominance of K2 (31.4%), K57 (18.6%), K64 (10.0%), K1 (5.7%) were isolated from patients of the Moscow neurosurgery ICU in 2014-2019. The rate of multi-drug resistant (MDR) and carbapenem-resistant phenotypes were 84.3% and 45.7%, respectively. Whole-genome sequencing of five selected strains belonging to cKp (ST395K47 and ST147K64), hvKp (ST86K2), and hvKp-MDR (ST23K1 and ST23K57) revealed blaSHV, blaTEM, blaCTX, blaOXA-48, and blaNDM beta-lactamase genes; acr, oqx, kpn, kde, and kex efflux genes; and K. pneumoniae virulence genes. Selective pressure of 100 mg/L ampicillin or 10 mg/L ceftriaxone induced changes of expression levels for named genes in the strains belonging to cKp, hvKp, and hybrid hvKp-MDR. Obtained results seem to be important for epidemiologists and clinicians for enhancing knowledge about hospital pathogens.
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Luo YC, Hsieh YC, Wu JW, Quyen TLT, Chen YY, Liao WC, Li SW, Wang SH, Pan YJ. Exploring the association between capsular types, sequence types, and carbapenemase genes in Acinetobacter baumannii. Int J Antimicrob Agents 2021; 59:106470. [PMID: 34757135 DOI: 10.1016/j.ijantimicag.2021.106470] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 08/31/2021] [Accepted: 10/24/2021] [Indexed: 11/24/2022]
Abstract
Acinetobacter baumannii is the main cause of nosocomial infections, and the treatment of such infections has become more difficult due to the emergence of carbapenem resistance. This study focused on major carbapenemase genes and explored the association between carbapenemase genes, sequence types (ST types), and capsular types (K types). A total of 98 carbapenem-resistant A. baumannii (CRAB) strains were collected from two hospitals, the Chang Gung Memorial Hospital-Lin Kou branch (LCGMH) in northern Taiwan and the CGMH-Kaohsiung branch (KCGMH) in southern Taiwan, from 2015-2017. Major carbapenemase genes of class A, B, and D β-lactamases were detected by polymerase chain reaction. All strains except 1 were positive for blaOXA-51-like, 76 strains (77.6%) carried blaOXA-23-like, and 25 strains (25.5%) carried blaOXA-24-like. The regional distribution showed that blaOXA-23-like was more predominant than blaOXA-24-like in both hospitals (85.3% and 60% in LCGMH and KCGMH, respectively); however, blaOXA-24-like displayed a much higher percentage in KCGMH (46.7%) than in LCGMH (16.2%). Oxford multilocus sequence typing and global optimal eBURST analysis were conducted for 59 strains. We revealed the association between blaOXA gene patterns, ST types, and K types and demonstrated that four major K types, KL2, KL10, KL22, and KL52, which were associated with specific ST types, were mainly clustered into clonal complexes CC208 and CC549 (a unique clonal complex found in Taiwan). These findings provide important information for monitoring the epidemiology and dissemination of this pathogen.
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Affiliation(s)
- Yun-Cong Luo
- Department of Microbiology and Immunology, School of Medicine, College of Medicine, China Medical University, Taichung, Taiwan
| | - Yu-Chia Hsieh
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Jia-Wen Wu
- Department of Microbiology and Immunology, School of Medicine, College of Medicine, China Medical University, Taichung, Taiwan
| | - Tran Lam Tu Quyen
- Department of Microbiology and Immunology, School of Medicine, College of Medicine, China Medical University, Taichung, Taiwan
| | - Yi-Yin Chen
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Wei-Chao Liao
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan; Department of Nephrology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Shiao-Wen Li
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Shi-Heng Wang
- Departments of Occupational Safety and Health and Public Health, College of Public Health, China Medical University, Taichung, Taiwan
| | - Yi-Jiun Pan
- Department of Microbiology and Immunology, School of Medicine, College of Medicine, China Medical University, Taichung, Taiwan.
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Kim JM, Fukushima Y, Yoshida H, Kim JS, Takahashi T. Comparative genomic features of Streptococcus canis based on the pan-genome orthologous group analysis according to sequence type. Jpn J Infect Dis 2021; 75:269-276. [PMID: 34588372 DOI: 10.7883/yoken.jjid.2021.533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Using bacterial pan-genome obtained through whole genome sequencing (WGS), coding DNA sequences (CDSs) can be clustered into pan-genome orthologous groups (POGs). We aimed to investigate comparative genomic features of Streptococcus canis based on POG analysis and to determine CDSs specific to prevalent sequence type (ST) 9. Twenty WGS datasets on S. canis strains from invasive and non-invasive specimens were retrieved from the National Center for Biotechnology Information Assembly database. Based on the WGS data, we performed comparative genome hybridization (CGH), pan- and core-genome prediction, Venn diagram test with five ST9 strains, and phylogenetic analysis, with ST determination. We compared the CDSs between seven ST9 and 13 non-ST9 strains. We observed genomic diversity based on CGH and Venn diagram. The predicted pan- and core-genomes contained 4,772 and 1,403 genes, respectively. We found five clades consisting of different STs (ST1, ST44/2, ST13/14, ST21/15/41, and ST9) based on phylogenetic tree. There were differences in four pathways (DNA restriction-modification system, DNA-mediated transposition, extracellular region, and response to oxidative stress) regulated by CDSs specific to ST9. Our findings describe genomic diversity in CGH and Venn diagram, pan- and core-genomes, five clades of genomes consisting of different STs, and unique CDS features associated to ST9.
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Affiliation(s)
- Jung-Min Kim
- Department of Laboratory Medicine, Kangdong Sacred Heart Hospital, Hallym University College of Medicine, Republic of Korea
| | - Yasuto Fukushima
- Laboratory of Infectious Diseases, Graduate School of Infection Control Sciences & Ōmura Satoshi Memorial Institute, Kitasato University, Japan
| | - Haruno Yoshida
- Laboratory of Infectious Diseases, Graduate School of Infection Control Sciences & Ōmura Satoshi Memorial Institute, Kitasato University, Japan
| | - Jae-Seok Kim
- Department of Laboratory Medicine, Kangdong Sacred Heart Hospital, Hallym University College of Medicine, Republic of Korea
| | - Takashi Takahashi
- Laboratory of Infectious Diseases, Graduate School of Infection Control Sciences & Ōmura Satoshi Memorial Institute, Kitasato University, Japan
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Zhang K, Ge H, He J, Hu M, Xu Z, Jiao X, Chen X. Salmonella Typhimurium ST34 Isolate Was More Resistant than the ST19 Isolate in China, 2007 - 2019. Foodborne Pathog Dis 2021; 19:62-69. [PMID: 34520252 DOI: 10.1089/fpd.2021.0047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
To disclose the antimicrobial susceptibility and wide adaptability of commonly occurring genotypes of Salmonella enterica serovar Typhimurium, the antimicrobial resistance and multilocus sequence typing (MLST) profiles of 196 Salmonella Typhimurium isolates (136 from food-producing animals, 19 from environments, 15 from markets, and 26 from humans) in China between 2007 and 2019 were analyzed. Tests of susceptibility to 19 antimicrobial agents using the broth microdilution method showed that 84.7% of the isolates were resistant to at least one antimicrobial. Antimicrobial susceptibility analysis demonstrated that 66.8% of the isolates were multidrug-resistant (MDR) strains, with resistance to three or more antimicrobials. The highest antidrug resistance was to ampicillin, amoxicillin/clavulanic acid, and tetracycline. Three MLST types were detected, and sequence type (ST) 19 was the most common ST. However, ST34 was associated with a higher MDR rate and more complex MDR patterns, than ST19 and ST99, although the exact mechanism has not been reported. Our study highlights the variation of drug resistance and STs from different sources and the association between STs and drug resistance, providing useful information for epidemiological research and developing a public health strategy.
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Affiliation(s)
- Kai Zhang
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality of Ministry of Agriculture and Rural Affairs, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Haojie Ge
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality of Ministry of Agriculture and Rural Affairs, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Jingjing He
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality of Ministry of Agriculture and Rural Affairs, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Maozhi Hu
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality of Ministry of Agriculture and Rural Affairs, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Zhengzhong Xu
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality of Ministry of Agriculture and Rural Affairs, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Xin'an Jiao
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality of Ministry of Agriculture and Rural Affairs, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Xiang Chen
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality of Ministry of Agriculture and Rural Affairs, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
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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: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Liu Z, Liu Y, Xi W, Liu S, Liu J, Mu H, Chen B, He H, Fan Y, Ma W, Zhang W, Fu M, Wang J, Song X. Genetic Features of Plasmid- and Chromosome-Mediated mcr-1 in Escherichia coli Isolates From Animal Organs With Lesions. Front Microbiol 2021; 12:707332. [PMID: 34456890 PMCID: PMC8386294 DOI: 10.3389/fmicb.2021.707332] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 07/08/2021] [Indexed: 11/22/2022] Open
Abstract
The genomic context of the mcr-1 gene in Escherichia coli from animal feces has been widely reported. However, less is known about the mcr-1-carrying plasmid characteristics and other functional regions of Escherichia coli isolates from animal organs with lesions. The present study investigated the antimicrobial resistance, population structure, and genetic features of mcr-1-positive Escherichia coli strains isolated from animal organs with lesions. The antimicrobial susceptibility testing indicated that 24 mcr-1-positive Escherichia coli isolates were resistant to at least three or all antimicrobial categories. MLST analysis suggested that the dominant clone complexes (CC) were mainly CC156, CC448, and CC10. In addition, ST10596, a newly discovered sequence type in swine, failed to be classified. Meanwhile, the mcr-1 gene located on the different plasmids was successfully transferred to the recipients, and whole-genome sequencing indicated the mcr-1 gene was embedded in mcr-1-pap2 cassette but not flanked by ISApl1. The mcr-1 gene is located on the chromosome and embedded in Tn6330. Furthermore, NDM-5 was found on the IncX3-type plasmid of J-8. The virB6 and traI gene of type IV secretion system (T4SS) were truncated by IS2 and IS100 and located on the IncX4- and the IncHI2/HI2A/N-type plasmids, respectively. The multidrug-resistant (MDR) region of IncHI2/HI2A/N-type plasmids contained two class 1 integrons (In0, In640) and four composite transposons (Tn4352, Tn6010, cn_4692_IS26, cn_6354_IS26). Overall, 24 mcr-1-positive Escherichia coli isolates in our study showed MDR, or even extensively drug resistant (XDR), and exhibited population diversity. The T4SS gene truncation by the insertion sequence may affect the efficiency of plasmid conjugative transfer. Furthermore, the class 1 integrons and composite transposons in the MDR region of IncHI2/HI2A/n-type plasmid contributed to the multireplicon plasmid formation, the acquisition, and transfer of antimicrobial resistance genes (ARGs).
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Affiliation(s)
- Zengyuan Liu
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Yingqiu Liu
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Wei Xi
- Qingdao Adverse Drug Reaction Monitoring Center, China Qingdao Institute for Food and Drug Control, Qingdao, China
| | - Shuangshi Liu
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Jia Liu
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Hailong Mu
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Beibei Chen
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Hao He
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Yunpeng Fan
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Wuren Ma
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Weimin Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Mingzhe Fu
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Juan Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Xiaoping Song
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
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Fursova NK, Astashkin EI, Ershova ON, Aleksandrova IA, Savin IA, Novikova TS, Fedyukina GN, Kislichkina AA, Fursov MV, Kuzina ES, Biketov SF, Dyatlov IA. Multidrug-Resistant Klebsiella pneumoniae Causing Severe Infections in the Neuro-ICU. Antibiotics (Basel) 2021; 10:antibiotics10080979. [PMID: 34439029 PMCID: PMC8389041 DOI: 10.3390/antibiotics10080979] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/09/2021] [Accepted: 08/13/2021] [Indexed: 11/16/2022] Open
Abstract
The purpose of this study was the identification of genetic lineages and antimicrobial resistance (AMR) and virulence genes in Klebsiella pneumoniae isolates associated with severe infections in the neuro-ICU. Susceptibility to antimicrobials was determined using the Vitek-2 instrument. AMR and virulence genes, sequence types (STs), and capsular types were identified by PCR. Whole-genome sequencing was conducted on the Illumina MiSeq platform. It was shown that K. pneumoniae isolates of ST14K2, ST23K57, ST39K23, ST76K23, ST86K2, ST218K57, ST219KL125/114, ST268K20, and ST2674K47 caused severe systemic infections, including ST14K2, ST39K23, and ST268K20 that were associated with fatal incomes. Moreover, eight isolates of ST395K2 and ST307KL102/149/155 were associated with manifestations of vasculitis and microcirculation disorders. Another 12 K. pneumoniae isolates of ST395K2,KL39, ST307KL102/149/155, and ST147K14/64 were collected from patients without severe systemic infections. Major isolates (n = 38) were XDR and MDR. Beta-lactamase genes were identified: blaSHV (n = 41), blaCTX-M (n = 28), blaTEM (n = 21), blaOXA-48 (n = 21), blaNDM (n = 1), and blaKPC (n = 1). The prevalent virulence genes were wabG (n = 41), fimH (n = 41), allS (n = 41), and uge (n = 34), and rarer, detected only in the genomes of the isolates causing severe systemic infections-rmpA (n = 8), kfu (n = 6), iroN (n = 5), and iroD (n = 5) indicating high potential of the isolates for hypervirulence.
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Affiliation(s)
- Nadezhda K. Fursova
- Department of Molecular Microbiology, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia; (E.I.A.); (T.S.N.)
- Correspondence:
| | - Evgenii I. Astashkin
- Department of Molecular Microbiology, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia; (E.I.A.); (T.S.N.)
| | - Olga N. Ershova
- Department of Clinical Epidemiology, National Medical Research Center of Neurosurgery Named after Academician N.N. Burdenko, 125047 Moscow, Russia; (O.N.E.); (I.A.A.); (I.A.S.)
| | - Irina A. Aleksandrova
- Department of Clinical Epidemiology, National Medical Research Center of Neurosurgery Named after Academician N.N. Burdenko, 125047 Moscow, Russia; (O.N.E.); (I.A.A.); (I.A.S.)
| | - Ivan A. Savin
- Department of Clinical Epidemiology, National Medical Research Center of Neurosurgery Named after Academician N.N. Burdenko, 125047 Moscow, Russia; (O.N.E.); (I.A.A.); (I.A.S.)
| | - Tatiana S. Novikova
- Department of Molecular Microbiology, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia; (E.I.A.); (T.S.N.)
| | - Galina N. Fedyukina
- Department of Immunobiochemistry of Pathogenic Microorganisms, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia; (G.N.F.); (S.F.B.)
| | - Angelina A. Kislichkina
- Department of Culture Collection, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia;
| | - Mikhail V. Fursov
- Department of Training and Improvement of Specialists, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia; (M.V.F.); (E.S.K.)
| | - Ekaterina S. Kuzina
- Department of Training and Improvement of Specialists, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia; (M.V.F.); (E.S.K.)
| | - Sergei F. Biketov
- Department of Immunobiochemistry of Pathogenic Microorganisms, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia; (G.N.F.); (S.F.B.)
| | - Ivan A. Dyatlov
- Department of Administration, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia;
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Jayasinghearachchi HS, Francis VR, Sathkumara HD, Krishnananthasivam S, Masakorala J, Muthugama T, De Silva AD, Corea EM. Nonclonal Burkholderia pseudomallei Population in Melioidosis Case Cluster, Sri Lanka. Emerg Infect Dis 2021; 27:2955-2957. [PMID: 34379585 PMCID: PMC8545001 DOI: 10.3201/eid2711.210219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
A melioidosis case cluster of 10 blood culture–positive patients occurred in eastern Sri Lanka after an extreme weather event. Four infections were caused by Burkholderia pseudomallei isolates of sequence type 594. Whole-genome analysis showed that the isolates were genetically diverse and the case cluster was nonclonal.
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