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Karunakaran S, Pless LL, Ayres AM, Ciccone C, Penzelik J, Sundermann AJ, Martin EM, Griffith MP, Waggle K, Hodges JC, Harrison LH, Snyder GM. Impact of discontinuation of contact precautions on surveillance- and whole genome sequencing-defined methicillin-resistant Staphylococcus aureus healthcare-associated infections. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2024; 4:e97. [PMID: 38836046 PMCID: PMC11149034 DOI: 10.1017/ash.2024.89] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/19/2024] [Accepted: 04/23/2024] [Indexed: 06/06/2024]
Abstract
Objective Prior studies evaluating the impact of discontinuation of contact precautions (DcCP) on methicillin-resistant Staphylococcus aureus (MRSA) outcomes have characterized all healthcare-associated infections (HAIs) rather than those likely preventable by contact precautions. We aimed to analyze the impact of DcCP on the rate of MRSA HAI including transmission events identified through whole genome sequencing (WGS) surveillance. Design Quasi experimental interrupted time series. Setting Acute care medical center. Participants Inpatients. Methods The effect of DcCP (use of gowns and gloves) for encounters among patients with MRSA carriage was evaluated using time series analysis of MRSA HAI rates from January 2019 through December 2022, compared to WGS-defined attributable transmission events before and after DcCP in December 2020. Results The MRSA HAI rate was 4.22/10,000 patient days before and 2.98/10,000 patient days after DcCP (incidence rate ratio [IRR] 0.71 [95% confidence interval 0.56-0.89]) with a significant immediate decrease (P = .001). There were 7 WGS-defined attributable transmission events before and 11 events after DcCP (incident rate ratio 0.90 [95% confidence interval 0.30-2.55]). Conclusions DcCP did not result in an increase in MRSA HAI or, in WGS-defined attributable transmission events. Comprehensive analyses of the effect of transmission prevention measures should include outcomes specifically measuring transmission-associated HAI.
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Affiliation(s)
- Sharon Karunakaran
- Division of Pediatric Infectious Diseases, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Lora Lee Pless
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Microbial Genomics Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ashley M Ayres
- Department of Infection Prevention and Control, UPMC Presbyterian/Shadyside, Pittsburgh, PA, USA
| | - Carl Ciccone
- Department of Infection Prevention and Control, UPMC Presbyterian/Shadyside, Pittsburgh, PA, USA
| | - Joseph Penzelik
- Department of Infection Prevention and Control, UPMC Presbyterian/Shadyside, Pittsburgh, PA, USA
| | - Alexander J Sundermann
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Microbial Genomics Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Elise M Martin
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Veterans' Affairs Pittsburgh Healthcare System, Pittsburgh, PA, USA
| | - Marissa P Griffith
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Microbial Genomics Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kady Waggle
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Microbial Genomics Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Lee H Harrison
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Microbial Genomics Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Graham M Snyder
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Infection Prevention and Control, UPMC Presbyterian/Shadyside, Pittsburgh, PA, USA
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2
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Zheng J, Liu L, Chen G, Xu W, Huang Y, Lei G, Huang W, Lv H, Yang X. Molecular Characteristics of Staphylococcus aureus Isolates form Food-Poisoning Outbreaks (2011-2022) in Sichuan, China. Foodborne Pathog Dis 2024; 21:323-330. [PMID: 38237168 DOI: 10.1089/fpd.2023.0097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024] Open
Abstract
Staphylococcal food poisoning (SFP) is one of the most common foodborne diseases in the world. This study aimed to investigate the molecular epidemiological characteristics of Staphylococcus aureus isolated from SFP. A total of 103 S. aureus isolates were obtained during 2011-2022 in Sichuan, southwest China. All isolates were tested for the genomic characteristics and phylogenetic analysis by performing whole-genome sequencing. Multilocus sequence typing analysis showed 17 multilocus sequence types (STs), ST7 (23.30%), ST5 (22.33%), and ST6 (16.50%) being the most common. A total of 45 virulence genes were detected, 22 of which were staphylococcal enterotoxin (SE) genes. Among the identified SE genes, selX exhibited the highest prevalence (86.4%). All isolates carried at least one SE gene. The results of the antimicrobial resistance (AMR) gene detection revealed 41 AMR genes of 12 classes. β-lactam resistance genes (blal, blaR1, blaZ) and tetracycline resistance gene (tet(38)) exhibited a higher prevalence rate. Core genome single nucleotide polymorphism showed phylogenetic clustering of the isolates with the same region, year, and ST. The results indicated that the SFP isolates in southwest of China harbored multiple toxin and resistance genes, with a high prevalence of new SEs. Therefore, it is important to monitor the antimicrobial susceptibility and SE of S. aureus to reduce the potential risks to public health.
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Affiliation(s)
- Jie Zheng
- College of Public Health, Southwest Medical University, Luzhou, China
- Center for Disease Control and Prevention of Sichuan Province, Chengdu, China
| | - Li Liu
- Center for Disease Control and Prevention of Sichuan Province, Chengdu, China
| | - Guo Chen
- Center for Disease Control and Prevention of Mianyang City, Mianyang, China
| | - Wenping Xu
- Center for Disease Control and Prevention of Luzhou City, Luzhou, China
| | - Yulan Huang
- Center for Disease Control and Prevention of Sichuan Province, Chengdu, China
| | - Gaopeng Lei
- Center for Disease Control and Prevention of Sichuan Province, Chengdu, China
| | - Weifeng Huang
- Center for Disease Control and Prevention of Sichuan Province, Chengdu, China
| | - Hong Lv
- Center for Disease Control and Prevention of Sichuan Province, Chengdu, China
| | - Xiaorong Yang
- College of Public Health, Southwest Medical University, Luzhou, China
- Center for Disease Control and Prevention of Sichuan Province, Chengdu, China
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3
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Sulikowska M, Marek A, Jarosz ŁS, Pyzik E, Stępień-Pyśniak D, Hauschild T. Pathogenic Potential of Coagulase-Positive Staphylococcus Strains Isolated from Aviary Capercaillies and Free-Living Birds in Southeastern Poland. Animals (Basel) 2024; 14:295. [PMID: 38254464 PMCID: PMC10812641 DOI: 10.3390/ani14020295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
The aim of the study was to determine the occurrence and characteristics of coagulase-positive Staphylococcus strains in the carcasses of wild birds and aviary capercaillies in Southeastern Poland. In total, samples taken from 333 birds were examined. The material consisted of swabs from the internal organs of dead birds (heart, liver, and spleen), the tarsal joints, and mucous membranes (conjunctiva and palatine fissure), as well as from unhatched embryos. The isolated Staphylococcus strains were tested for sensitivity to nine antimicrobial agents and the presence of selected virulence genes. An analysis of the similarity of isolates within species was performed using pulsed-field gel electrophoresis (PFGE). The result indicates that coagulase-positive strains accounted for 5.7% and belonged to the species: Staphylococcus aureus, Staphylococcus pseudintermedius, and Staphylococcus delphini. Among isolated strains, 15.8% were multidrug resistant. The most frequently detected virulence genes were hla in 58% of isolates and hlb and hld in 47.4% of isolates. The results of multiplex PCR showed the presence of genes responsible for the production of enterotoxins C, B, E, and J, in single isolates. It can be concluded that coagulase-positive Staphylococcus strains accounted for a small percentage of staphylococci isolated from free-living birds in the study area. The occurrence of multidrug-resistant coagulase-positive Staphylococcus strains in aviary capercaillies suggests that they play a role in the transmission and spread of resistant strains into the environment. Free-living birds may also be a reservoir of enterotoxigenic Staphylococcus strains.
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Affiliation(s)
| | - Agnieszka Marek
- Department of Preventive Veterinary and Avian Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, 20-950 Lublin, Poland; (E.P.)
| | - Łukasz Sebastian Jarosz
- Department of Epizootiology and Clinic of Infectious Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, 20-612 Lublin, Poland
| | - Ewelina Pyzik
- Department of Preventive Veterinary and Avian Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, 20-950 Lublin, Poland; (E.P.)
| | - Dagmara Stępień-Pyśniak
- Department of Preventive Veterinary and Avian Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, 20-950 Lublin, Poland; (E.P.)
| | - Tomasz Hauschild
- Department of Microbiology and Biotechnology, Faculty of Biology, University of Bialystok, 15-245 Białystok, Poland
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4
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Westgeest AC, Schippers EF, Rosema S, Fliss MA, Kuijper EJ, Zwittink RD, Lokate M, Wouthuyzen-Bakker M, Lambregts MMC, Bathoorn E. Genetic Determinants in MRSA Carriage and Their Association with Decolonization Outcome. Curr Microbiol 2024; 81:63. [PMID: 38217690 PMCID: PMC10787693 DOI: 10.1007/s00284-023-03581-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 12/01/2023] [Indexed: 01/15/2024]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) colonization increases the risk of infection. Response to decolonization treatment is highly variable and determinants for successful decolonization or failure of eradication treatment are largely unknown. Insight into genetic predictors of eradication failure is potentially useful in clinical practice. The aim of this study was to explore genetic characteristics that are associated with MRSA decolonization failure. This cohort study was performed in a tertiary care hospital in the Netherlands. Patients with ≥ 1 positive MRSA culture from any site and with available whole -genome sequencing data of the MRSA isolate between 2017 and 2022 were included. Lineages, resistance, and virulence factors were stratified by MRSA decolonization outcome. In total, 56 patients were included: 12/56 (21%) with treatment failure and 44/56 (79%) with successful decolonization (with or without preceding treatment). A significant association was found between ciprofloxacin-resistant lineages and failure of eradication (OR 4.20, 95%CI 1.11-15.96, P = 0.04). Furthermore, livestock-associated MRSA and the major community-associated MRSA lineages ST6-t304 and ST8-t008 were associated with successful eradication treatment or spontaneous clearance. In conclusion, this explorative study showed a higher eradication failure rate in complicated MRSA carriers with ciprofloxacin-resistant MRSA lineages, which are predominantly healthcare-associated. Further studies are warranted to confirm the higher eradication failure risk of ciprofloxacin-resistant lineages, and identify the underlying mechanisms.
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Affiliation(s)
- Annette C Westgeest
- Department of Infectious Diseases, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands.
| | - Emile F Schippers
- Department of Infectious Diseases, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
- Department of Internal Medicine, Haga Teaching Hospital, Els Borst-Eilersplein 275, 2545 AA, The Hague, The Netherlands
| | - Sigrid Rosema
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Monika A Fliss
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Ed J Kuijper
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Antonie Van Leeuwenhoeklaan 9, 3721 MA, Bilthoven, The Netherlands
| | - Romy D Zwittink
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Antonie Van Leeuwenhoeklaan 9, 3721 MA, Bilthoven, The Netherlands
| | - Mariëtte Lokate
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Marjan Wouthuyzen-Bakker
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Merel M C Lambregts
- Department of Infectious Diseases, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Erik Bathoorn
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
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Tao L, Zhang X, Wang X, Ding J. Using molecular methods to delineate norovirus outbreaks: a systematic review. Arch Virol 2024; 169:16. [PMID: 38172375 DOI: 10.1007/s00705-023-05953-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 11/14/2023] [Indexed: 01/05/2024]
Abstract
Noroviruses are among the major causative agents of human acute gastroenteritis, and the nature of norovirus outbreaks can differ considerably. The number of single-nucleotide polymorphisms (SNPs) between strains is used to assess their relationships. There is currently no universally accepted cutoff value for clustering strains that define an outbreak or linking the individuals involved. This study was conducted to estimate the threshold value of genomic variations among related strains within norovirus outbreaks. We carried out a literature search in the PubMed and Web of Science databases. SNP rates were defined as the number of SNPs/sequence length (bp) × 100%. The Mann-Whitney U-test was used in comparisons of the distribution of SNP rates for different sequence regions, genogroups (GI and GII), transmission routes, and sequencing methods. A total of 25 articles reporting on 108 norovirus outbreaks were included. In 99.1% of the outbreaks, the SNP rates were below 0.50%, and in 89.8%, the SNP rates were under 0.20%. Outbreak strains showed higher SNP rates when the P2 domain was used for sequence analysis (Z = -2.652, p = 0.008) and when an NGS method was used (Z = -3.686, p < 0.001). Outbreaks caused by different norovirus genotypes showed no significant difference in SNP rates. Compared with person-to-person outbreaks, SNP rates were lower in common-source outbreaks, but no significant difference was found when differences in sequencing methods were taken into consideraton. SNP rates under 0.20% and 0.50% could be considered as the rigorous and relaxed threshold, respectively, of strain similarity within a norovirus outbreak. More data are needed to evaluate differences within and between various norovirus outbreaks.
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Affiliation(s)
- Luqiu Tao
- Nanjing Municipal Center for Disease Control and Prevention affiliated to Nanjing Medical University, Zizhulin 2, 210003, Nanjing, Jiangsu, China
- School of Public Health, Nanjing Medical University, 101 Longmian Avenue, 211166, Nanjing, Jiangsu, China
| | - Xinyang Zhang
- Nanjing Municipal Center for Disease Control and Prevention affiliated to Nanjing Medical University, Zizhulin 2, 210003, Nanjing, Jiangsu, China
- School of Public Health, Nanjing Medical University, 101 Longmian Avenue, 211166, Nanjing, Jiangsu, China
| | - Xuan Wang
- Nanjing Municipal Center for Disease Control and Prevention affiliated to Nanjing Medical University, Zizhulin 2, 210003, Nanjing, Jiangsu, China
| | - Jie Ding
- Nanjing Municipal Center for Disease Control and Prevention affiliated to Nanjing Medical University, Zizhulin 2, 210003, Nanjing, Jiangsu, China.
- School of Public Health, Nanjing Medical University, 101 Longmian Avenue, 211166, Nanjing, Jiangsu, China.
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6
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Zhu Z, Wu S, Chen X, Tan W, Zou G, Huang Q, Meng X, Hu DL, Li S. Heterogeneity and transmission of food safety-related enterotoxigenic Staphylococcus aureus in pig abattoirs in Hubei, China. Microbiol Spectr 2023; 11:e0191323. [PMID: 37772855 PMCID: PMC10581196 DOI: 10.1128/spectrum.01913-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 08/04/2023] [Indexed: 09/30/2023] Open
Abstract
The dissemination of Staphylococcus aureus in the pork production chain is a major food safety concern. Abattoirs can serve both as disruptor and transmitter for S. aureus. In this study, we conducted a systematic genomic epidemiology research on the prevalence, heterogeneity, and transmission of S. aureus in 3,638 samples collected from four pig abattoirs in Hubei province, China. Our findings revealed substantial heterogeneity between S. aureus recovered from samples collected at upstream (from stunning step to head-removal step) and downstream (from splitting step to chilling step) locations within the slaughter process. Overall, 966 (26.6%) samples were positive for S. aureus, with significantly higher overall prevalence for upstream samples (29.0%, 488/1,681) compared to downstream samples (24.4%, 478/1,957). Antimicrobial susceptibility testing demonstrated that the isolates from the upstream exhibited significantly higher resistance proportions to different antimicrobials than those from the downstream. Whole-genome sequencing of 126 isolates revealed that ST398 (32.9%, 23/70) and ST9 (22.9%, 16/70) were more common among upstream isolates, while ST7 (35.7%, 20/56) and ST97 (28.6%, 16/56) were most frequently observed among downstream isolates. Additionally, molecular characterization analysis demonstrated that upstream isolates possessed significantly higher enterotoxigenic potential, more antimicrobial resistance genes, and S. aureus pathogenicity islands than downstream isolates. Notably, we discovered that enterotoxigenic S. aureus could be transmitted across different slaughter stages, with knives, water, and air serving as vectors. Although slaughtering processes had a substantial effect on reducing the food safety risk posed by enterotoxigenic S. aureus, the possibility of its widespread transmission should not be disregarded. IMPORTANCE Staphylococcus aureus (S. aureus) is one of the most important foodborne pathogens, and can cause foodborne poisoning by producing enterotoxins. Pork is a preferable reservoir and its contamination often occurs during the slaughter process. Our findings revealed significant differences in the prevalence, antimicrobial resistance, and enterotoxigenic potential between the upstream and downstream isolates within the slaughter process. Also, it is imperative not to overlook enterotoxigenic S. aureus transmitted across all stages of the slaughter process, with notable vectors being knives, water, and air. These findings hold significant implications for policy-makers to reassess their surveillance projects, and underscore the importance of implementing effective control measures to minimize the risk of S. aureus contamination in pork production. Moreover, we provide a more compelling method of characterizing pathogen transmission based on core-SNPs of bacterial genomes.
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Affiliation(s)
- Zhihao Zhu
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Simin Wu
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Xingyu Chen
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Wei Tan
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Geng Zou
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Qi Huang
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Xianrong Meng
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Dong-Liang Hu
- Department of Zoonoses, Kitasato University School of Veterinary Medicine, Towada, Japan
| | - Shaowen Li
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
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Wu X, Li X, Yu J, Shen M, Fan C, Lu Y, Gao J, Li X, Li H. Outbreak of OXA-232-producing carbapenem-resistant Klebsiella pneumoniae ST15 in a Chinese teaching hospital: a molecular epidemiological study. Front Cell Infect Microbiol 2023; 13:1229284. [PMID: 37671147 PMCID: PMC10475586 DOI: 10.3389/fcimb.2023.1229284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 08/03/2023] [Indexed: 09/07/2023] Open
Abstract
Background and Aims The incidence of OXA-232-producing carbapenem-resistant Klebsiella pneumoniae (CRKP) has been on the rise in China over the past five years, potentially leading to nosocomial epidemics. This study investigates the first outbreak of CRKP in the Second Affiliated Hospital of Jiaxing University. Methods Between February 2021 and March 2022, 21 clinical isolates of OXA-232-producing CRKP were recovered from 16 patients in the Second Affiliated Hospital of Jiaxing University. We conducted antimicrobial susceptibility tests, whole genome sequencing, and bioinformatics to determine the drug resistance profile of these clinical isolates. Results Whole-genome sequencing revealed that all 21 OXA-232-producing CRKP strains belonged to the sequence type 15 (ST15) and shared similar resistance, virulence genes, and plasmid types, suggesting clonal transmission between the environment and patients. Integrated genomic and epidemiological analysis traced the outbreak to two clonal transmission clusters, cluster 1 and cluster 2, including 14 and 2 patients. It was speculated that the CRKP transmission mainly occurred in the ICU, followed by brain surgery, neurosurgery, and rehabilitation department. Phylogenetic analysis indicated that the earliest outbreak might have started at least a year before the admission of the index patient, and these strains were closely related to those previously isolated from two major adjacent cities, Shanghai and Hangzhou. Comparative genomics showed that the IncFII-type and IncHI1B-type plasmids of cluster 2 had homologous recombination at the insertion sequence sites compared with the same type of plasmids in cluster 1, resulting in the insertion of 4 new drug resistance genes, including TEM-1, APH(6)-Id, APH(3'')-Ib and sul2. Conclusions Our study observed the clonal spread of ST15 OXA-232-producing between patients and the hospital environment. The integration of genomic and epidemiological data offers valuable insights and facilitate the control of nosocomial transmission.
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Affiliation(s)
- Xiaoyan Wu
- Department of Laboratory Medicine, the Second Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
| | - Xiangchen Li
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research, Hangzhou, Zhejiang, China
| | - Junjie Yu
- Department of Laboratory Medicine, the Second Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
| | - Mengli Shen
- Department of Laboratory Medicine, the Second Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
| | - Chenliang Fan
- Department of Laboratory Medicine, the Second Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
| | - Yewei Lu
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research, Hangzhou, Zhejiang, China
| | - Junshun Gao
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research, Hangzhou, Zhejiang, China
| | - Xiaosi Li
- Department of Laboratory Medicine, the Second Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
| | - Hongsheng Li
- Department of Laboratory Medicine, the Second Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
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Ding X, Fu X, Euphrasie D, Ferroni A, Sermet-Gaudelus I, Charbit A, Coureuil M, Jamet A. Genomic analysis of Staphylococcus aureus sequential isolates from lungs of patients with cystic fibrosis. Microbes Infect 2023; 25:105124. [PMID: 36871931 DOI: 10.1016/j.micinf.2023.105124] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 02/24/2023] [Indexed: 03/07/2023]
Abstract
Staphylococcus aureus is the predominant pathogen in children with cystic fibrosis (CF) in France and, around 80% of them harbored S. aureus in their lungs. This study investigated virulence and antimicrobial resistance-associated genes and within-host evolution polymorphisms in 14 S. aureus persistent clones from 14 chronically infected CF children. For each of the 14 patients, we compared genomes of two isogenic sequential isolates separated by 2-9 years. All isolates were methicillin-sensitive and harbored the immune evasion gene cluster, whereas half of them harbored the enterotoxin gene cluster. Most clones were capsule type 8 (8/14) and accessory gene regulator (agr)-specificity group 1 (9/14). We identified convergent mutations in genes involved in carbohydrate metabolism, cell wall metabolism, genetic information processing and adhesion, which are likely to play important role in intracellular invasion and persistence. Further explorations relying notably on proteomics will contribute to improve our understanding of the mechanisms at play in the striking long-term persistence ability of S. aureus.
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Affiliation(s)
- Xiongqi Ding
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, F75015 Paris, France
| | - Xiali Fu
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, F75015 Paris, France
| | - Daniel Euphrasie
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, F75015 Paris, France
| | - Agnes Ferroni
- Department of Clinical Microbiology, Necker-Enfants Malades Hospital, AP-HP Centre Université de Paris, F75015 Paris, France
| | - Isabelle Sermet-Gaudelus
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, F75015 Paris, France
| | - Alain Charbit
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, F75015 Paris, France
| | - Mathieu Coureuil
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, F75015 Paris, France
| | - Anne Jamet
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, F75015 Paris, France; Department of Clinical Microbiology, Necker-Enfants Malades Hospital, AP-HP Centre Université de Paris, F75015 Paris, France.
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9
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Snoussi M, Noumi E, Bouali N, Bazaid AS, Alreshidi MM, Altayb HN, Chaieb K. Antibiotic Susceptibility Profiling of Human Pathogenic Staphylococcus aureus Strains Using Whole Genome Sequencing and Genome-Scale Annotation Approaches. Microorganisms 2023; 11:1124. [PMID: 37317098 DOI: 10.3390/microorganisms11051124] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 04/22/2023] [Accepted: 04/24/2023] [Indexed: 06/16/2023] Open
Abstract
Staphylococcus species are major pathogens with increasing importance due to the rise in antibiotic resistance. Whole genome sequencing and genome-scale annotation are promising approaches to study the pathogenicity and dissemination of virulence factors in nosocomial methicillin-resistant and multidrug-resistant bacteria in intensive care units. Draft genome sequences of eight clinical S. aureus strains were assembled and annotated for the prediction of antimicrobial resistance genes, virulence factors, and phylogenetic analysis. Most of the studied S. aureus strains displayed multi-resistance toward the tested drugs, reaching more than seven drugs up to 12 in isolate S22. The mecA gene was detected in three isolates (S14, S21, and S23), mecC was identified in S8 and S9, and blaZ was commonly identified in all isolates except strain S23. Additionally, two complete mobile genomic islands coding for methicillin resistance SCCmec Iva (2B) were identified in strains S21 and S23. Numerous antimicrobial resistance genes (norA, norC, MgrA, tet(45), APH(3')-IIIa, and AAC(6')-APH(2″)) were identified in chromosomes of different strains. Plasmid analysis revealed the presence of blaZ, tetK, and ermC in different plasmid types, located in gene cassettes containing plasmid replicons (rep) and insertion sequences (IS). Additionally, the aminoglycoside-resistant determinants were identified in S1 (APH(3')-IIIa), while AAC(6)-APH(2″) was detected in strains S8 and S14. The trimethoprim (dfrC) resistance gene was detected in S. aureus S21, and the fosfomycin (fosB) resistance gene was detected only in S. aureus S14. We also noted that S. aureus S1 belongs to ST1-t127, which has been reported as one of the most frequent human pathogen types. Additionally, we noted the presence of rare plasmid-mediated mecC-MRSA in some of our isolates.
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Affiliation(s)
- Mejdi Snoussi
- Department of Biology, College of Science, University of Ha'il, Ha'il P.O. Box 2440, Saudi Arabia
- Medical and Diagnostic Research Centre, University of Ha'il, Ha'il 55473, Saudi Arabia
| | - Emira Noumi
- Department of Biology, College of Science, University of Ha'il, Ha'il P.O. Box 2440, Saudi Arabia
- Medical and Diagnostic Research Centre, University of Ha'il, Ha'il 55473, Saudi Arabia
| | - Nouha Bouali
- Department of Biology, College of Science, University of Ha'il, Ha'il P.O. Box 2440, Saudi Arabia
- Medical and Diagnostic Research Centre, University of Ha'il, Ha'il 55473, Saudi Arabia
| | - Abdulrahman S Bazaid
- Department of Medical, Laboratory Science, College of Applied Medical Sciences, University of Ha'il, Ha'il 55476, Saudi Arabia
| | - Mousa M Alreshidi
- Department of Biology, College of Science, University of Ha'il, Ha'il P.O. Box 2440, Saudi Arabia
- Medical and Diagnostic Research Centre, University of Ha'il, Ha'il 55473, Saudi Arabia
| | - Hisham N Altayb
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Center of Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Kamel Chaieb
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Laboratory of Analysis, Treatment and Valorization of Pollutants of the Environmental and Products, Faculty of Pharmacy, University of Monastir, Monastir 5000, Tunisia
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Silvola J, Gröndahl-Yli-Hannuksela K, Hirvioja T, Rantakokko-Jalava K, Rintala E, Auranen K, Junnila J, Marttila H, Lindholm L, Vuopio J. Whole genome sequencing reveals new links between spa t172/CC59 methicillin-resistant Staphylococcus aureus cases in low-endemicity region of Southwest Finland, 2007‒2016. Sci Rep 2022; 12:21326. [PMID: 36494398 PMCID: PMC9734107 DOI: 10.1038/s41598-022-25556-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) rates have remained relatively low in Finland. In Southwest Finland, however, annual MRSA incidence increased from 12 to 25/100,000 between 2007 and 2016 with spa t172 strain causing one fourth (237/983) of all cases. This provoked us to study the molecular epidemiology of t172-MRSA, aiming to better understand the transmission of this strain type. We combined epidemiological data and whole genome sequencing (WGS) of a set of 64 (27%, 64/237) t172-MRSA isolates covering 10 years. Isolates represented sporadic and index cases of all identified healthcare-associated outbreaks (HAOs) and family clusters (FCs). Among the included 62 isolates, core-genome MLST analysis revealed eight genomic clusters comprising 24 (38.7%) isolates and 38 (61.3%) non-clustered isolates. Cluster 1 comprised ten and the remaining seven clusters two isolates each, respectively. Two epidemiologically distinct HAOs were linked in cluster 1. FCs were involved in all clusters. All strains were associated with epidemic clonal complex CC59. We were able to confirm the spread of several successful t172-MRSA subclones in regional healthcare and the community. WGS complemented routine surveillance by revealing undetected links between t172-MRSA cases. Targeted, WGS-based typing could enhance MRSA surveillance without the need for routine WGS diagnostics.
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Affiliation(s)
- Jaakko Silvola
- grid.1374.10000 0001 2097 1371Institute of Biomedicine, University of Turku, Turku, Finland
| | | | - Tiina Hirvioja
- grid.410552.70000 0004 0628 215XDepartment of Hospital Hygiene & Infection Control, Turku University Hospital, Turku, Finland
| | - Kaisu Rantakokko-Jalava
- grid.410552.70000 0004 0628 215XClinical Microbiology Laboratory, Turku University Hospital, Turku, Finland
| | - Esa Rintala
- grid.410552.70000 0004 0628 215XDepartment of Hospital Hygiene & Infection Control, Turku University Hospital, Turku, Finland
| | - Kari Auranen
- grid.1374.10000 0001 2097 1371Department of Mathematics and Statistics and Department of Clinical Medicine, University of Turku, Turku, Finland
| | - Jenna Junnila
- grid.1374.10000 0001 2097 1371Institute of Biomedicine, University of Turku, Turku, Finland
| | - Harri Marttila
- grid.410552.70000 0004 0628 215XDepartment of Hospital Hygiene & Infection Control, Turku University Hospital, Turku, Finland
| | - Laura Lindholm
- grid.14758.3f0000 0001 1013 0499Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Jaana Vuopio
- grid.1374.10000 0001 2097 1371Institute of Biomedicine, University of Turku, Turku, Finland ,grid.410552.70000 0004 0628 215XClinical Microbiology Laboratory, Turku University Hospital, Turku, Finland ,grid.14758.3f0000 0001 1013 0499Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
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11
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Sánchez-Serrano A, García-González N, Bonillo D, Ruiz-Hueso P, Villanova R, Campo-Bes I, Tormo N, Salvador C, Gimeno C, González-Candelas F. Molecular Epidemiology of Methicillin-Resistant Staphylococcus aureus in a Tertiary Hospital from the Comunidad Valenciana (Spain). Microb Drug Resist 2022; 28:1071-1078. [DOI: 10.1089/mdr.2022.0027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Andrea Sánchez-Serrano
- Joint Research Unit Infection and Public Health FISABIO-University Valencia, Institute for Integrative Systems Biology I2SysBio (CSIC-UV), Valencia, Spain
| | - Neris García-González
- Joint Research Unit Infection and Public Health FISABIO-University Valencia, Institute for Integrative Systems Biology I2SysBio (CSIC-UV), Valencia, Spain
| | - Daniel Bonillo
- Joint Research Unit Infection and Public Health FISABIO-University Valencia, Institute for Integrative Systems Biology I2SysBio (CSIC-UV), Valencia, Spain
| | - Paula Ruiz-Hueso
- Joint Research Unit Infection and Public Health FISABIO-University Valencia, Institute for Integrative Systems Biology I2SysBio (CSIC-UV), Valencia, Spain
| | - Rebeca Villanova
- Joint Research Unit Infection and Public Health FISABIO-University Valencia, Institute for Integrative Systems Biology I2SysBio (CSIC-UV), Valencia, Spain
| | - Israel Campo-Bes
- Joint Research Unit Infection and Public Health FISABIO-University Valencia, Institute for Integrative Systems Biology I2SysBio (CSIC-UV), Valencia, Spain
| | - Nuria Tormo
- Microbiology Department, Consorcio Hospital General Universitario de Valencia, Valencia, Spain
| | - Carme Salvador
- Microbiology Department, Consorcio Hospital General Universitario de Valencia, Valencia, Spain
| | - Concepción Gimeno
- Microbiology Department, Consorcio Hospital General Universitario de Valencia, Valencia, Spain
| | - Fernando González-Candelas
- Joint Research Unit Infection and Public Health FISABIO-University Valencia, Institute for Integrative Systems Biology I2SysBio (CSIC-UV), Valencia, Spain
- CIBER in Epidemiology and Public Health, Valencia, Spain
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12
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Biggs SL, Jennison AV, Bergh H, Graham R, Nimmo G, Whiley D. Limited evidence of patient-to-patient transmission of Staphylococcus aureus strains between children with cystic fibrosis, Queensland, Australia. PLoS One 2022; 17:e0275256. [PMID: 36206247 PMCID: PMC9543978 DOI: 10.1371/journal.pone.0275256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 09/13/2022] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVES Here we used whole genome sequencing (WGS) to understand strain diversity and potential for patient-to-patient transmission of Staphylococcus aureus among children with cystic fibrosis (CF) in Queensland, Australia. METHODS S. aureus isolates (n = 401) collected between January 2018 and April 2019 from 184 patients with CF (n = 318 isolates) and 76 patients without CF (n = 83 isolates) were subjected to WGS and subsequent multilocus sequence typing (MLST), and a phylogeny was constructed from core genome single nucleotide polymorphism (SNP) analysis. The subsequent data was compared with available patient information. RESULTS WGS revealed that patients with CF were essentially colonised by the same genotypes as those seen in patients without CF. Sequence types (ST) for our patients with CF were predominantly ST5 (20.1%), ST30 (7.3%), ST15 (6.3%) and ST8 (5.3%). Two Australian clones, ST93 and ST239, typically seen in skin infections and health-care settings, respectively, were notably absent from our patients with CF. Based on a SNP distance threshold of 14 SNPs, 20 cluster types involving 50/260 patients were evident; of these, 6 clusters contained only patients found to be siblings or otherwise living in the same household. Epidemiological relationships could not be determined for a remaining 14 cluster types involving 38 patients, comprising 2-7 (median 2) patients each. Multiple S. aureus genotypes were observed in 19/73 CF patients who provided more than one sample. CONCLUSION These results show that WGS is a useful tool for surveillance of S. aureus strains in children with CF and that the strains in our CF cohort were largely consistent with those circulating in patients without CF. Overall, this confirms previous findings and indicates that S. aureus acquisition in children with CF is similar to that of other patient groups, with limited evidence of potential patient-to-patient transmission within this patient group.
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Affiliation(s)
- Sharon L. Biggs
- School of Medicine, The University of Queensland, UQ Centre for Clinical Research (UQCCR), Herston, Queensland, Australia
| | - Amy V. Jennison
- Public and Environmental Health, Forensic and Scientific Services, Coopers Plains, Queensland, Australia
| | - Haakon Bergh
- Pathology Queensland Central Laboratory, Herston, Queensland, Australia
| | - Rikki Graham
- Public and Environmental Health, Forensic and Scientific Services, Coopers Plains, Queensland, Australia
| | - Graeme Nimmo
- School of Medicine, Griffith University, Gold Coast, Queensland, Australia
| | - David Whiley
- School of Medicine, The University of Queensland, UQ Centre for Clinical Research (UQCCR), Herston, Queensland, Australia
- Pathology Queensland Central Laboratory, Herston, Queensland, Australia
- * E-mail:
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13
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Afzal M, Vijay AK, Stapleton F, Willcox MDP. Genomics of Staphylococcus aureus Strains Isolated from Infectious and Non-Infectious Ocular Conditions. Antibiotics (Basel) 2022; 11:antibiotics11081011. [PMID: 36009880 PMCID: PMC9405196 DOI: 10.3390/antibiotics11081011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 01/08/2023] Open
Abstract
Staphylococcus aureus is a major cause of ocular infectious (corneal infection or microbial keratitis (MK) and conjunctivitis) and non-infectious corneal infiltrative events (niCIE). Despite the significant morbidity associated with these conditions, there is very little data about specific virulence factors associated with the pathogenicity of ocular isolates. A set of 25 S. aureus infectious and niCIEs strains isolated from USA and Australia were selected for whole genome sequencing. Sequence types and clonal complexes of S. aureus strains were identified by using multi-locus sequence type (MLST). The presence or absence of 128 virulence genes was determined by using the virulence finder database (VFDB). Differences between infectious (MK + conjunctivitis) and niCIE isolates from USA and Australia for possession of virulence genes were assessed using the chi-square test. The most common sequence types found among ocular isolates were ST5, ST8 while the clonal complexes were CC30 and CC1. Virulence genes involved in adhesion (ebh, clfA, clfB, cna, sdrD, sdrE), immune evasion (chp, esaD, esaE, esxB, esxC, esxD), and serine protease enzymes (splA, splD, splE, splF) were more commonly observed in infectious strains (MK + conjunctivitis) than niCIE strains (p = 0.004). Toxin genes were present in half of infectious (49%, 25/51) and niCIE (51%, 26/51) strains. USA infectious isolates were significantly more likely to possess splC, yent1, set9, set11, set36, set38, set40, lukF-PV, and lukS-PV (p < 0.05) than Australian infectious isolates. MK USA strains were more likely to possesses yent1, set9, set11 than USA conjunctivitis strains (p = 0.04). Conversely USA conjunctivitis strains were more likely to possess set36 set38, set40, lukF-PV, lukS-PV (p = 0.03) than MK USA strains. The ocular strain set was then compared to 10 fully sequenced non-ocular S. aureus strains to identify differences between ocular and non-ocular isolates. Ocular isolates were significantly more likely to possess cna (p = 0.03), icaR (p = 0.01), sea (p = 0.001), set16 (p = 0.01), and set19 (p = 0.03). In contrast non-ocular isolates were more likely to possess icaD (p = 0.007), lukF-PV, lukS-PV (p = 0.01), selq (p = 0.01), set30 (p = 0.01), set32 (p = 0.02), and set36 (p = 0.02). The clones ST5, ST8, CC30, and CC1 among ocular isolates generally reflect circulating non-ocular pathogenic S. aureus strains. The higher rates of genes in infectious and ocular isolates suggest a potential role of these virulence factors in ocular diseases.
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14
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Lawal OU, Ayobami O, Abouelfetouh A, Mourabit N, Kaba M, Egyir B, Abdulgader SM, Shittu AO. A 6-Year Update on the Diversity of Methicillin-Resistant Staphylococcus aureus Clones in Africa: A Systematic Review. Front Microbiol 2022; 13:860436. [PMID: 35591993 PMCID: PMC9113548 DOI: 10.3389/fmicb.2022.860436] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 03/15/2022] [Indexed: 11/13/2022] Open
Abstract
Background Methicillin-resistant Staphylococcus aureus (MRSA) is a leading cause of hospital-associated (HA) and community-associated (CA) infections globally. The multi-drug resistant nature of this pathogen and its capacity to cause outbreaks in hospital and community settings highlight the need for effective interventions, including its surveillance for prevention and control. This study provides an update on the clonal distribution of MRSA in Africa. Methods A systematic review was conducted by screening for eligible English, French, and Arabic articles from November 2014 to December 2020, using six electronic databases (PubMed, EBSCOhost, Web of Science, Scopus, African Journals Online, and Google Scholar). Data were retrieved and analyzed according to the Preferred Reporting Items for Systematic Review and Meta-Analysis guidelines (registered at PROSPERO: CRD42021277238). Genotyping data was based primarily on multilocus sequence types (STs) and Staphylococcal Cassette Chromosome mec (SCCmec) types. We utilized the Phyloviz algorithm in the cluster analysis and categorization of the MRSA STs into various clonal complexes (CCs). Results We identified 65 studies and 26 publications from 16 of 54 (30%) African countries that provided sufficient genotyping data. MRSA with diverse staphylococcal protein A (spa) and SCCmec types in CC5 and CC8 were reported across the continent. The ST5-IV [2B] and ST8-IV [2B] were dominant clones in Angola and the Democratic Republic of Congo (DRC), respectively. Also, ST88-IV [2B] was widely distributed across the continent, particularly in three Portuguese-speaking countries (Angola, Cape Verde, and São Tomé and Príncipe). The ST80-IV [2B] was described in Algeria and Egypt, while the HA-ST239/ST241-III [3A] was only identified in Egypt, Ghana, Kenya, and South Africa. ST152-MRSA was documented in the DRC, Kenya, Nigeria, and South Africa. Panton-Valentine leukocidin (PVL)-positive MRSA was observed in several CCs across the continent. The median prevalence of PVL-positive MRSA was 33% (ranged from 0 to 77%; n = 15). Conclusion We observed an increase in the distribution of ST1, ST22, and ST152, but a decline of ST239/241 in Africa. Data on MRSA clones in Africa is still limited. There is a need to strengthen genomic surveillance capacity based on a "One-Health" strategy to prevent and control MRSA in Africa.
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Affiliation(s)
- Opeyemi Uwangbaoje Lawal
- Laboratory of Bacterial Evolution and Molecular Epidemiology, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa (ITQB-NOVA), Oeiras, Portugal
| | - Olaniyi Ayobami
- Unit for Healthcare-Associated Infections, Surveillance of Antimicrobial Resistance and Consumption, Robert Koch Institute, Berlin, Germany
| | - Alaa Abouelfetouh
- Department of Microbiology and Immunology, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt.,Department of Microbiology and Immunology, Faculty of Pharmacy, AlAlamein International University, Alalamein, Egypt
| | - Nadira Mourabit
- Biotechnology, Environmental Technology and Valorisation of Bio-Resources Team, Department of Biology, Faculty of Sciences and Techniques of Al Hoceima, Abdelmalek Essaadi University, Tetouan, Morocco
| | - Mamadou Kaba
- Division of Medical Microbiology, Department of Clinical Laboratory Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Beverly Egyir
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Shima M Abdulgader
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa
| | - Adebayo Osagie Shittu
- Department of Microbiology, Obafemi Awolowo University, Ile-Ife, Nigeria.,Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
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15
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Kinnevey PM, Kearney A, Shore AC, Earls MR, Brennan GI, Poovelikunnel TT, Humphreys H, Coleman DC. Meticillin-susceptible Staphylococcus aureus transmission among healthcare workers, patients and the environment in a large acute hospital under non-outbreak conditions investigated using whole-genome sequencing. J Hosp Infect 2022; 127:15-25. [PMID: 35594983 DOI: 10.1016/j.jhin.2022.05.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 11/26/2022]
Abstract
BACKGROUND The role of meticillin-resistant Staphylococcus aureus (MSSA) colonization of healthcare workers (HCWs), patients and the hospital environment in MSSA transmission events (TEs) is poorly understood. AIMS We recently investigated these roles for MRSA under non-outbreak conditions in a large hospital with a history of endemic MRSA over two years using whole-genome sequencing (WGS). Numerous potential MRSA TEs were identified. Here we investigated MSSA TEs from the same sources during the same two-year hospital study. METHODS HCW (N=326) and patient (N=388) volunteers on nine wards were tested for nasal and oral MSSA colonization over two years. Near-patient environment (N=1,164), high-frequency touch sites (N=810) and air (N=445) samples were screened for MSSA. Representative MSSA and clinical isolates were sequenced and analysed by core-genome multilocus-sequence typing (cgMLST). Closely related isolates (≤24 allelic differences) were segregated into related-isolated groups (RIGs). Potential TEs involving MSSA in RIGs from HCWs, patients and patient infections were identified in combination with epidemiological data FINDINGS: In total, 635 MSSA were recovered: clinical isolates (N=82), HCWs (N=170), patients (N=120), environmental isolates (N=263). Twenty-four clonal complexes (CCs) were identified among 406/635 MSSA sequenced, of which 183/406 segregated into 59 RIGs. Numerous potential HCW-to-patient, HCW-to-HCW and patient-to-patient TEs were identified, predominantly among CC5-MSSA, CC30-MSSA and CC45-MSSA. HCW, patient, clinical and environmental isolates were identified in 33, 24, six and 32 RIGs, respectively, with 19/32 of these containing MSSA related to HCW and/or patient isolates. CONCLUSIONS WGS detected numerous potential hospital MSSA TEs involving HCWs, patients and environmental contamination under non-outbreak conditions.
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Affiliation(s)
- P M Kinnevey
- Microbiology Research Unit, Division of Oral Biosciences, Dublin Dental University Hospital, University of Dublin, Trinity College Dublin, Dublin, Ireland
| | - A Kearney
- Microbiology Research Unit, Division of Oral Biosciences, Dublin Dental University Hospital, University of Dublin, Trinity College Dublin, Dublin, Ireland; Department of Infection Control and Prevention, Beaumont Hospital, Dublin, Ireland
| | - A C Shore
- Microbiology Research Unit, Division of Oral Biosciences, Dublin Dental University Hospital, University of Dublin, Trinity College Dublin, Dublin, Ireland
| | - M R Earls
- Microbiology Research Unit, Division of Oral Biosciences, Dublin Dental University Hospital, University of Dublin, Trinity College Dublin, Dublin, Ireland
| | - G I Brennan
- National MRSA Reference Laboratory, St. James's Hospital, Dublin, Ireland
| | - T T Poovelikunnel
- Department of Infection Control and Prevention, Beaumont Hospital, Dublin, Ireland; Department of Clinical Microbiology, Royal College of Surgeons in Ireland
| | - H Humphreys
- Department of Clinical Microbiology, Royal College of Surgeons in Ireland; Department of Microbiology, Beaumont Hospital, Dublin, Ireland
| | - D C Coleman
- Microbiology Research Unit, Division of Oral Biosciences, Dublin Dental University Hospital, University of Dublin, Trinity College Dublin, Dublin, Ireland.
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Oh S, Nam SK, Chang HE, Park KU. Comparative Analysis of Short- and Long-Read Sequencing of Vancomycin-Resistant Enterococci for Application to Molecular Epidemiology. Front Cell Infect Microbiol 2022; 12:857801. [PMID: 35463637 PMCID: PMC9019564 DOI: 10.3389/fcimb.2022.857801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/17/2022] [Indexed: 11/13/2022] Open
Abstract
Vancomycin-resistant enterococci (VRE) are nosocomial pathogens with genetic plasticity and widespread antimicrobial resistance (AMR). To prevent the spread of VRE in the hospital setting, molecular epidemiological approaches such as pulsed-field gel electrophoresis and multilocus sequence typing have been implemented for pathogen outbreak surveillance. However, due to the insufficient discriminatory power of these methods, whole-genome sequencing (WGS), which enables high-resolution analysis of entire genomic sequences, is being used increasingly. Herein, we performed WGS of VRE using both short-read next-generation sequencing (SR-NGS) and long-read next-generation sequencing (LR-NGS). Since standardized workflows and pipelines for WGS-based bacterial epidemiology are lacking, we established three-step pipelines for SR- and LR-NGS, as a standardized WGS-based approach for strain typing and AMR profiling. For strain typing, we analyzed single-nucleotide polymorphisms (SNPs) of VRE isolates and constructed SNP-based maximum-likelihood phylogenies. The phylogenetic trees constructed using short and long reads showed good correspondence. Still, SR-NGS exhibited higher sensitivity for detecting nucleotide substitutions of bacterial sequences. During AMR profiling, we examined AMR genes and resistance-conferring mutations. We also assessed the concordance between genotypic and phenotypic resistance, which was generally better for LR-NGS than SR-NGS. Further validation of our pipelines based on outbreak cases is necessary to ensure the overall performance of pipelines.
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Affiliation(s)
- Sujin Oh
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Soo Kyung Nam
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Ho Eun Chang
- Department of Research and Development, PHiCS Institute, Seoul, South Korea
| | - Kyoung Un Park
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, South Korea
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
- *Correspondence: Kyoung Un Park,
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Primary Isolation of Mycobacterium ulcerans. Methods Mol Biol 2021. [PMID: 34643898 DOI: 10.1007/978-1-0716-1779-3_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Primary isolation of Mycobacterium ulcerans is the separation and growth of the bacterium from a mixed population either in clinical specimen or environmental specimen in pure cultures. It is a crucial activity as it can be used to monitor antimicrobial treatment, surveillance for antimicrobial resistance, and molecular epidemiology studies toward understanding pathogen ecology and transmission as well as pathogen biology. The process involves removal of unwanted fast-growing bacteria using 5% oxalic acid, inoculation on Lowenstein-Jensen medium supplemented with glycerol, and incubation at temperatures between 30 °C and 33 °C.
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Kinnevey PM, Kearney A, Shore AC, Earls MR, Brennan G, Poovelikunnel TT, Humphreys H, Coleman DC. Meticillin-resistant Staphylococcus aureus transmission among healthcare workers, patients and the environment in a large acute hospital under non-outbreak conditions investigated using whole-genome sequencing. J Hosp Infect 2021; 118:99-107. [PMID: 34428508 DOI: 10.1016/j.jhin.2021.08.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 08/03/2021] [Indexed: 11/16/2022]
Abstract
BACKGROUND The role of meticillin-resistant Staphylococcus aureus (MRSA) colonization of healthcare workers (HCWs), patients and the hospital environment in MRSA transmission in non-outbreak settings is poorly understood. AIMS To investigate transmission events (TEs) involving HCWs, patients and the environment under non-outbreak conditions in a hospital with a history of endemic MRSA using whole-genome sequencing (WGS). METHODS HCW (N = 326) and patient (N = 388) volunteers on nine wards were tested for nasal and oral MRSA colonization over two years. Near-patient environment (N = 1164), high-frequency touch sites (N = 810) and air (N = 445) samples were screened for MRSA. Representative MRSA and clinical isolates were analysed by WGS and core-genome multi-locus sequence typing (cgMLST). Closely related isolates (≤24 allelic differences) were segregated into related isolated groups (RIGs). FINDINGS In total, 155 MRSA were recovered: clinical isolates (N = 41), HCWs (N = 22), patients (N = 37), environmental isolates (N = 55). Nine clonal complexes (CCs) were identified among 110/155 MRSA sequenced with 77/110 assigned to CC22. Seventy-nine MRSA segregated into 17 RIGs. Numerous potential TEs were associated with CC22-MRSA (RIGs 1-15), CC45-MRSA (RIG-16) and CC8-MRSA (RIG-17). RIG-1, (the largest RIG) contained 24 ST22-MRSA-IVh from six HCWs, six patients, four clinical and eight environmental samples recovered over 17 months involving 7/9 wards. TEs involving HCW-to-patient, HCW-to-HCW, patient-to-patient and environmental contamination by HCW/patient isolates were evident. HCW, patient, clinical and environmental isolates were identified in four, nine, seven and 13 RIGs, respectively, with 12/13 of these containing isolates closely related to HCW and/or patient isolates. CONCLUSIONS WGS detected numerous potential hospital MRSA TEs involving HCWs, patients and the environment under non-outbreak conditions.
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Affiliation(s)
- P M Kinnevey
- Microbiology Research Unit, Division of Oral Biosciences, Dublin Dental University Hospital, University of Dublin, Trinity College Dublin, Dublin, Ireland
| | - A Kearney
- Microbiology Research Unit, Division of Oral Biosciences, Dublin Dental University Hospital, University of Dublin, Trinity College Dublin, Dublin, Ireland; Department of Infection Control and Prevention, Beaumont Hospital, Dublin, Ireland
| | - A C Shore
- Microbiology Research Unit, Division of Oral Biosciences, Dublin Dental University Hospital, University of Dublin, Trinity College Dublin, Dublin, Ireland
| | - M R Earls
- Microbiology Research Unit, Division of Oral Biosciences, Dublin Dental University Hospital, University of Dublin, Trinity College Dublin, Dublin, Ireland
| | - G Brennan
- National MRSA Reference Laboratory, St James's Hospital, Dublin, Ireland
| | - T T Poovelikunnel
- Department of Infection Control and Prevention, Beaumont Hospital, Dublin, Ireland; Department of Clinical Microbiology, Royal College of Surgeons in Ireland, Ireland
| | - H Humphreys
- Department of Clinical Microbiology, Royal College of Surgeons in Ireland, Ireland; Department of Microbiology, Beaumont Hospital, Dublin, Ireland
| | - D C Coleman
- Microbiology Research Unit, Division of Oral Biosciences, Dublin Dental University Hospital, University of Dublin, Trinity College Dublin, Dublin, Ireland.
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19
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Konstantinovski MM, Veldkamp KE, Lavrijsen APM, Bosch T, Kraakman MEM, Nooij S, Claas ECJ, Gooskens J. Hospital transmission of borderline oxacillin-resistant Staphylococcus aureus evaluated by whole-genome sequencing. J Med Microbiol 2021; 70. [PMID: 34269673 PMCID: PMC8493421 DOI: 10.1099/jmm.0.001384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction Staphylococcus aureus is a major cause of hospital infections worldwide. Awareness towards methicillin-resistant S. aureus (MRSA) infections is high but attention towards borderline oxacillin-resistant S. aureus (BORSA) is limited, possibly due to an underestimated clinical relevance, presumption of low incidence and diagnostic limitations. Gap statement BORSA surveillance has not been routinely implemented, and thus consensus with regard to a definition and infection control measures is lacking. Aim Our goals were to investigate the occurrence, molecular characteristics and clinical manifestations of BORSA infections in the hospital setting. Methodology Following an increased incidence in 2016, BORSA cases in 2014/2016 (in our institution) were more specifically evaluated. Medical records were reviewed to investigate epidemiological links, clinical characteristics and outcomes. Resistance and virulence markers were assessed by whole genome sequencing (WGS). Conventional methods: amplified fragment length polymorphism (AFLP) ; multilocus sequence typing (MLST) and multiple locus variable-number tandem repeat analysis (MLVA) were compared with core genome MLST (cgMLST) and whole-genome single nucleotide polymorphism (wgSNP) analysis to confirm genetic clusters. Results From 2009 to 2013, BORSA comprised 0.1 % of all clinical S. aureus strains. In 2016, the incidence was six-fold higher in comparison to the baseline. Whole-genome SNP and cgMLST confirmed two BORSA clusters among patients with dermatological conditions. Patients with BORSA presented with skin infections, and one case developed a severe invasive infection with a fatal outcome. Infection control measures successfully prevented further transmission in both clusters. WGS findings showed that BORSA strains carried multiple resistance and virulence genes with increased pathogenic potential. Conclusion WGS and cgMLST effectively characterized and confirmed BORSA clusters among at-risk patients with clinical manifestations ranging from mild skin infections to life-threatening bacteraemia. Clinical awareness and active monitoring are therefore warranted for the timely implementation of infection control measures to prevent BORSA transmission in high-risk patients.
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Affiliation(s)
| | - Karin Ellen Veldkamp
- Medical Microbiology Department, Leiden University Medical Center, Leiden, Netherlands
| | | | - Thijs Bosch
- Infectious Diseases Research, Diagnostics and Laboratory Surveillance, National Institute for Public Health and the Environment, de Bilt, Netherlands
| | - Margriet E M Kraakman
- Medical Microbiology Department, Leiden University Medical Center, Leiden, Netherlands
| | - Sam Nooij
- Medical Microbiology Department, Leiden University Medical Center, Leiden, Netherlands
| | - Eric C J Claas
- Medical Microbiology Department, Leiden University Medical Center, Leiden, Netherlands
| | - Jairo Gooskens
- Medical Microbiology Department, Leiden University Medical Center, Leiden, Netherlands
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20
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Elliott TM, Hare N, Hajkowicz K, Hurst T, Doidge M, Harris PN, Gordon LG. Evaluating the economic effects of genomic sequencing of pathogens to prioritise hospital patients competing for isolation beds. AUST HEALTH REV 2021; 45:59-65. [PMID: 33049199 DOI: 10.1071/ah20071] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 05/18/2020] [Indexed: 11/23/2022]
Abstract
Objective This study compared the costs and patient movements of a new hospital protocol to discontinue contact precautions for patients with non-multiresistant methicillin-resistant Staphylococcus aureus (nmMRSA), based on whole-genome sequencing (WGS) of pathogens with current practice. Methods A hybrid simulation model was constructed and analysed over a 12-month time horizon. Six multidrug-resistant organisms and influenza were modelled concurrently where infected patients competed for isolation beds. Model inputs included pathogen incidence, resources for WGS, staff and contact precautions, hospital processes, room allocations and their associated costs. Data were sourced from aggregated records of patient admissions during 2017-18, clinical records and published reports. Results The WGS protocol resulted in 389 patients isolated (44% of current practice), 5223 'isolation bed days' (56%) and 268 closed-bed days (88%). Over 1 year, the mean (±s.d.) total cost for the WGS protocol was A$749243±126667; compared with current practice, the overall cost savings were A$690864±300464. Conclusion Using WGS to inform infection control teams of pathogen transmission averts patients from isolation rooms and reduces significant resources involved in implementing contact precautions. What is known about the topic? There are an estimated 265000 hospital-acquired infections (HAI) in Australia each year. WGS can accurately identify the genetic lineage among HAIs and determine transmission clusters that can help infection control staff manage patients. Economic appraisals are lacking to inform whether pathogen genomics services should be adopted within already-stretched hospital budgets. What does this paper add? An isolation protocol using pathogen genomics to provide additional information on the relatedness of a pathogen between colonised patients showed favourable results for healthcare costs and patient flow. Using WGS, in a confirmatory role, to discontinue certain patients from contact precautions and isolation rooms resulted in cost savings of A$690864 across 1 year for a single major hospital. What are the implications for practitioners? Using pathogen WGS services for infection control potentially curbs hospital spending, averts patient isolations and improves patient flow within hospitals.
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Affiliation(s)
- Thomas M Elliott
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Qld 4006, Australia. ; ; and Corresponding author.
| | - Nicole Hare
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Qld 4006, Australia. ;
| | - Krispin Hajkowicz
- Infectious Diseases Unit, Royal Brisbane and Women's Hospital, Butterfield Street, Herston, Qld 4029, Australia. ; ; ; and The University of Queensland, Centre for Clinical Research, Building 71/918, Royal Brisbane and Women's Hospital, Herston, Qld 4006, Australia.
| | - Trish Hurst
- Infectious Diseases Unit, Royal Brisbane and Women's Hospital, Butterfield Street, Herston, Qld 4029, Australia. ; ;
| | - Michelle Doidge
- Infectious Diseases Unit, Royal Brisbane and Women's Hospital, Butterfield Street, Herston, Qld 4029, Australia. ; ;
| | - Patrick N Harris
- The University of Queensland, Centre for Clinical Research, Building 71/918, Royal Brisbane and Women's Hospital, Herston, Qld 4006, Australia.
| | - Louisa G Gordon
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Qld 4006, Australia. ; ; and The University of Queensland, School of Public Health, 266 Herston Road, Herston, Qld 4006, Australia; and Queensland University of Technology, School of Nursing, QUT N Block, Ring Road, Kelvin Grove, Qld 4059, Australia
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21
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Karampatakis T, Papadopoulos P, Tsergouli K, Angelidis AS, Sergelidis D, Papa A. Genetic characterization of two methicillin-resistant Staphylococcus aureus spa type t127 strains isolated from workers in the dairy production chain in Greece. Acta Microbiol Immunol Hung 2021:2021.01460. [PMID: 34133323 DOI: 10.1556/030.2021.01460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/27/2021] [Indexed: 01/22/2023]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) constitutes a constant threat for the public health. Aim of the present study was to analyse the whole genome sequences of two MRSA strains belonging to Staphylococcus protein A (spa) type t127 isolated from humans working in two distantly located dairy production farms in Greece.MRSA strains were isolated from the nasal cavity of a food handler in a milk industry in Epirus, northwestern Greece (E-MRSA), and a person working in a cattle farm in Thrace, northeastern Greece (T-MRSA). Whole genome sequences taken using next generation sequencing were analysed for resistance and virulence genes applying various bioinformatic tools.Both isolates were assigned to ST1-IVa-t127 type, and they were transferring genes conferring resistance to tetracycline, β-lactams, and aminoglycosides; T-MRSA was carrying additional genes leading to macrolide, lincosamide and streptogramin B (MLSB) resistance. Both isolates were carrying three plasmid replicon types, rep5, rep7 and rep16, while T-MRSA harboured also rep10 and rep15. E-MRSA carried scn and sak genes which were absent from T-MRSA.In conclusion, the genetic characterization of two unrelated ST1-IVa-t127 MRSA strains isolated from humans in close contact with livestock in Greece can be used as basis for further epidemiological and evolutionary studies.
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Affiliation(s)
- Theodoros Karampatakis
- 1Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Greece
| | - Panagiotis Papadopoulos
- 2Laboratory of Food Hygiene-Veterinary Public Health, School of Veterinary Medicine, Aristotle University of Thessaloniki, Greece
| | - Katerina Tsergouli
- 1Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Greece
| | - Apostolos S Angelidis
- 3Laboratory of Safety and Quality of Milk and Dairy Products, School of Veterinary Medicine, Aristotle University of Thessaloniki, Greece
| | - Daniel Sergelidis
- 2Laboratory of Food Hygiene-Veterinary Public Health, School of Veterinary Medicine, Aristotle University of Thessaloniki, Greece
| | - Anna Papa
- 1Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Greece
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22
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Pimentel de Araujo F, Monaco M, Del Grosso M, Pirolo M, Visca P, Pantosti A. Staphylococcus aureus clones causing osteomyelitis: a literature review (2000-2020). J Glob Antimicrob Resist 2021; 26:29-36. [PMID: 33965630 DOI: 10.1016/j.jgar.2021.03.030] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 03/19/2021] [Accepted: 03/31/2021] [Indexed: 10/21/2022] Open
Abstract
OBJECTIVES Staphylococcus aureus is the most common causative organism of osteomyelitis (OM). Nevertheless, the molecular epidemiology of S. aureus causing OM remains ill-defined. This study aimed to address the global epidemiology of S. aureus clones from OM patients. METHODS Literature databases were searched for studies reporting the molecular typing of S. aureus involved in OM published between 1 January 2000 and 29 July 2020. Data from 32 articles that fulfilled the inclusion criteria were analysed for year of publication, country of patients, methicillin susceptibility and genotypic characteristics of S. aureus isolates. RESULTS Pandemic clones CC5, CC8, CC22, CC30 and CC45 were the most common in OM. The distribution of clones differed greatly among studies owing to the local epidemiology of S. aureus and the MSSA heterogeneity. PVL-positive MRSA clones belonging to ST80/CC80 and ST8/CC8/USA300 were the most common among paediatric patients in Europe and the USA; greater variability was observed in the adult population. In Europe, MRSA belonged to PVL-negative CC5, CC8 and CC22 indicating a nosocomial origin of infections; in Asia PVL-positive ST59/CC59 MRSA was the most frequent. PVL-positive clones were often detected in haematogenous OM in children and adults. Although MSSA were polyclonal, PVL-negative ST398/CC398 MSSA was the most prevalent clone in diabetic foot OM. CONCLUSION All major S. aureus clones circulating both in hospital and community settings appear to be capable of causing OM. Future studies reporting molecular typing and genomic data will provide more insights into the epidemiology and pathobiology of S. aureus clones causing OM.
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Affiliation(s)
- Fernanda Pimentel de Araujo
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy; Department of Science, Roma Tre University, Viale G. Marconi 446, 00146, Rome, Italy
| | - Monica Monaco
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy.
| | - Maria Del Grosso
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Mattia Pirolo
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146, Rome, Italy
| | - Paolo Visca
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146, Rome, Italy
| | - Annalisa Pantosti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
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23
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Johnson WL, Sohn MB, Taffner S, Chatterjee P, Dunman PM, Pecora N, Wozniak RAF. Genomics of Staphylococcus aureus ocular isolates. PLoS One 2021; 16:e0250975. [PMID: 33939761 PMCID: PMC8092774 DOI: 10.1371/journal.pone.0250975] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 04/16/2021] [Indexed: 02/02/2023] Open
Abstract
Staphylococcus aureus is a major cause of ocular infections, often resulting in devastating vision loss. Despite the significant morbidity associated with these infections, little is yet known regarding the specific strain types that may have a predilection for ocular tissues nor the set of virulence factors that drive its pathogenicity in this specific biological niche. Whole genome sequencing (WGS) can provide valuable insight in this regard by providing a prospective, comprehensive assessment of the strain types and virulence factors driving disease among specific subsets of clinical isolates. As such, a set of 163-member S. aureus ocular clinical strains were sequenced and assessed for both common strain types (multilocus sequence type (MLST), spa, agr) associated with ocular infections as well as the presence/absence of 235 known virulence factors in a high throughput manner. This ocular strain set was then directly compared to a fully sequenced 116-member non-ocular S. aureus strain set curated from NCBI in order to identify key differences between ocular and non-ocular S. aureus isolates. The most common sequence types found among ocular S. aureus isolates were ST5, ST8 and ST30, generally reflecting circulating non-ocular pathogenic S. aureus strains. However, importantly, ocular isolates were found to be significantly enriched for a set of enterotoxins, suggesting a potential role for this class of virulence factors in promoting ocular disease. Further genomic analysis revealed that these enterotoxins are located on mobile pathogenicity islands, thus horizontal gene transfer may promote the acquisition of enterotoxins, potentially amplifying S. aureus virulence in ocular tissues.
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Affiliation(s)
- William L. Johnson
- Department of Ophthalmology, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Michael B. Sohn
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Samantha Taffner
- Department of Clinical Microbiology, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Payel Chatterjee
- Department of Ophthalmology, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Paul M. Dunman
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Nicole Pecora
- Department of Clinical Microbiology, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Rachel A. F. Wozniak
- Department of Ophthalmology, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
- * E-mail:
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24
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Szarvas J, Bartels MD, Westh H, Lund O. Rapid Open-Source SNP-Based Clustering Offers an Alternative to Core Genome MLST for Outbreak Tracing in a Hospital Setting. Front Microbiol 2021; 12:636608. [PMID: 33868194 PMCID: PMC8047125 DOI: 10.3389/fmicb.2021.636608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/09/2021] [Indexed: 11/13/2022] Open
Abstract
Traditional genotyping methods for infection control of antimicrobial-resistant bacteria in healthcare settings have been supplemented by whole-genome sequencing (WGS), often relying on a gene-based approach, e.g., core genome multilocus sequence typing (cgMLST), to cluster-related samples. In this study, we compared clusters of methicillin-resistant Staphylococcus aureus (MRSA) and Enterococcus faecium analyzed with the commercial cgMLST software Ridom SeqSphere+ and with an open-source single-nucleotide polymorphism (SNP)-based phylogenetic analysis pipeline (PAPABAC). A total of 5,655 MRSA and 2,572 E. faecium patient isolates, collected between 2013 and 2018, were processed. Clusters of 1,844 MRSA and 1,355 E. faecium isolates were compared to cgMLST results, and epidemiological data were included when available. The phylogenies inferred by the two different technologies were highly concordant, and the MRSA SNP tree re-captured known hospital-related outbreaks and epidemiologically linked samples. PAPABAC has the advantage over Ridom SeqSphere+ to generate stable, referable clusters without the need for sequence assembly, and it is a free-of-charge, open-source alternative to the commercial software.
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Affiliation(s)
- Judit Szarvas
- Research Group for Genomic Epidemiology, Division for Global Surveillance, National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Mette Damkjaer Bartels
- MRSA Knowledge Center, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark.,Department of Clinical Microbiology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
| | - Henrik Westh
- Department of Clinical Microbiology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ole Lund
- Research Group for Genomic Epidemiology, Division for Global Surveillance, National Food Institute, Technical University of Denmark, Lyngby, Denmark
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25
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A narrative review of single-nucleotide polymorphism detection methods and their application in studies of Staphylococcus aureus. JOURNAL OF BIO-X RESEARCH 2021. [DOI: 10.1097/jbr.0000000000000071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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26
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Whole-genome sequencing for neonatal intensive care unit outbreak investigations: Insights and lessons learned. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY 2021; 1:e2. [PMID: 36168459 PMCID: PMC9495531 DOI: 10.1017/ash.2021.161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 12/20/2022]
Abstract
Abstract
Infectious diseases outbreaks are a cause of significant morbidity and mortality among hospitalized patients. Infants admitted to the neonatal intensive care unit (NICU) are particularly vulnerable to infectious complications during hospitalization. Thus, rapid recognition of and response to outbreaks in the NICU is essential. At Rush University Medical Center, whole-genome sequencing (WGS) has been utilized since early 2016 as an adjunctive method for outbreak investigations. The use of WGS and potential lessons learned are illustrated for 3 different NICU outbreak investigations involving methicillin-resistant Staphylococcus aureus (MRSA), group B Streptococcus (GBS), and Serratia marcescens. WGS has contributed to the understanding of the epidemiology of outbreaks in our NICU, and it has also provided further insight in settings of unusual diseases or when lower-resolution typing methods have been inadequate. WGS has emerged as the new gold standard for evaluating strain relatedness. As barriers to implementation are overcome, WGS has the potential to transform outbreak investigation in healthcare settings.
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27
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Ochoa SA, Cruz-Córdova A, Mancilla-Rojano J, Escalona-Venegas G, Esteban-Kenel V, Franco-Hernández I, Parra-Ortega I, Arellano-Galindo J, Hernández-Castro R, Perez-López CF, De la Rosa-Zamboni D, Xicohtencatl-Cortes J. Control of Methicillin-Resistant Staphylococcus aureus Strains Associated With a Hospital Outbreak Involving Contamination From Anesthesia Equipment Using UV-C. Front Microbiol 2020; 11:600093. [PMID: 33381094 PMCID: PMC7767929 DOI: 10.3389/fmicb.2020.600093] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 11/25/2020] [Indexed: 12/23/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is considered an opportunistic pathogen in humans and is mainly associated with healthcare-associated infections (HCAIs). This bacterium colonizes the skin and mucous membranes of healthy people and causes frequent hospital outbreaks. The aim of this study was to perform molecular typing of the staphylococcal cassette chromosome mec (SCCmec) and agr loci as wells as to establish the pulsotypes and clonal complexes (CCs) for MRSA and methicillin-sensitive S. aureus (MSSA) outbreaks associated with the operating room (OR) at a pediatric hospital. Twenty-five clinical strains of S. aureus (19 MRSA and 6 MSSA strains) were recovered from the outbreak (patients, anesthesia equipment, and nasopharyngeal exudates from external service anesthesia technicians). These clinical S. aureus strains were mainly resistant to benzylpenicillin (100%) and erythromycin (84%) and were susceptible to vancomycin and nitrofurantoin. The SCCmec type II was amplified in 84% of the S. aureus strains, and the most frequent type of the agr locus was agrII, which was amplified in 72% of the strains; however, the agrI and agrIII genes were mainly detected in MSSA strains. A pulsed-field gel electrophoresis (PFGE) analysis grouped the 25 strains into 16 pulsotypes (P), the most frequent of which was P1, including 10 MRSA strains related to the anesthesia equipment, external service anesthesia technicians, and hospitalized patients. Multilocus sequence typing (MLST) identified 15 sequence types (STs) distributed in nine CCs. The most prevalent ST was ST1011, belonging to CC5, which was associated with the SCCmec type II and agrII type. We postulate that the external service anesthesia technicians were MRSA carriers and that these strains were indirectly transmitted from the contaminated anesthesia equipment that was inappropriately disinfected. Finally, the MRSA outbreak was controlled when the anesthesia equipment disinfection was improved and hand hygiene was reinforced.
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Affiliation(s)
- Sara A Ochoa
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México Federico Gómez, Ciudad de México, Mexico
| | - Ariadnna Cruz-Córdova
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México Federico Gómez, Ciudad de México, Mexico
| | - Jetsi Mancilla-Rojano
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México Federico Gómez, Ciudad de México, Mexico.,Facultad de Medicina, Posgrado de Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Gerardo Escalona-Venegas
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México Federico Gómez, Ciudad de México, Mexico
| | - Veronica Esteban-Kenel
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México Federico Gómez, Ciudad de México, Mexico
| | - Isabel Franco-Hernández
- Laboratorio Central de Bacteriología, Hospital Infantil de México Federico Gómez, Ciudad de México, Mexico
| | - Israel Parra-Ortega
- Laboratorio Central de Bacteriología, Hospital Infantil de México Federico Gómez, Ciudad de México, Mexico
| | - José Arellano-Galindo
- Departamento de Infectología, Hospital Infantil de México Federico Gómez, Ciudad de México, Mexico
| | - Rigoberto Hernández-Castro
- Departamento de Ecología de Agentes Patógenos, Hospital General Dr. Manuel Gea González, Ciudad de México, Mexico
| | - Citlalli F Perez-López
- Departamento de Epidemiología Hospitalaria, Hospital Infantil de México Federico Gómez, Ciudad de México, Mexico
| | - Daniela De la Rosa-Zamboni
- Departamento de Epidemiología Hospitalaria, Hospital Infantil de México Federico Gómez, Ciudad de México, Mexico
| | - Juan Xicohtencatl-Cortes
- Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México Federico Gómez, Ciudad de México, Mexico
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28
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Konstantinovski MM, Bekker V, Kraakman MEM, Bruijning ML, van der Zwan CJ, Lopriore E, Veldkamp KE. Borderline oxacillin-resistant Staphylococcus aureus carriage among healthcare workers at neonatal intensive care unit and paediatric ward. J Hosp Infect 2020; 108:104-108. [PMID: 33245996 DOI: 10.1016/j.jhin.2020.11.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 11/19/2020] [Accepted: 11/20/2020] [Indexed: 10/22/2022]
Abstract
BACKGROUND During a meticillin-resistant Staphylococcus aureus contact tracing and screening investigation, two borderline oxacillin-resistant Staphylococcus aureus (BORSA)-positive screening cultures were encountered among neonatal intensive care unit (NICU) healthcare workers (HCWs). This finding led to further investigations. AIM To assess the likelihood of an outbreak with direct transmission among HCWs. METHODS An infection control team was initiated after the discovery. The team initiated additional infection control measures and evaluated new findings. All NICUs and paediatric ward HCWs were screened for BORSA carriage, and a prospective BORSA seven-week monitoring period for patients was observed. To assess the likelihood of an outbreak with direct transmission among HCWs, the BORSA isolates were analysed using augmented fragment length polymorphism and whole-genome sequencing (WGS). FINDINGS Positive HCWs were prohibited from clinical work while awaiting the results from the screening programme. In all, 127 NICU and 77 general paediatric ward HCWs were screened for BORSA carriage; five HCWs were BORSA positive. Seventy-two patients were screened during the seven-week period yielding a total of 138 cultures, ranging from one to nine cultures per patient. No spread from HCWs to patients occurred, and the BORSA screening programme was discontinued. WGS analysis with core genome multi-locus sequence typing of all five BORSA strains showed relatedness between two NICU strains. CONCLUSION During a seven-week period, no transmission from BORSA-positive HCWs to neonates was observed in either screening or clinical cultures. More vigilance and experience is needed to design adequate evidence-based interventions in the future for this vulnerable population.
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Affiliation(s)
| | - V Bekker
- Leiden University Medical Center, Leiden, The Netherlands
| | - M E M Kraakman
- Leiden University Medical Center, Leiden, The Netherlands
| | - M L Bruijning
- Leiden University Medical Center, Leiden, The Netherlands
| | | | - E Lopriore
- Leiden University Medical Center, Leiden, The Netherlands
| | - K E Veldkamp
- Leiden University Medical Center, Leiden, The Netherlands
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Mizusawa M, Carroll KC. Novel strategies for rapid identification and susceptibility testing of MRSA. Expert Rev Anti Infect Ther 2020; 18:759-778. [PMID: 32329637 DOI: 10.1080/14787210.2020.1760842] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
INTRODUCTION Methicillin-resistant Staphylococcus aureus (MRSA) is associated with adverse clinical outcomes and increased morbidity, mortality, length of hospital stay, and health-care costs. Rapid diagnosis of MRSA infections has been associated with positive impact on clinical outcomes. AREAS COVERED We searched relevant papers in PubMed for the last 10 years. In major papers, we scanned the bibliographies to ensure that important articles were included. This review describes screening and diagnostic test methods for MRSA and their analytical performances with a focus on rapid molecular-based assays including those that are on the horizon. Future novel technologies will allow more rapid detection of phenotypic resistance. In the case of whole-genome sequencing, detection of mutations may predict resistance, transmission, and virulence. EXPERT OPINION Currently there are many diagnostic options for the detection of MRSA in surveillance and clinical samples. In general, these are highly accurate and have resulted in improvements in targeted management and reduction in hospital or intensive care unit length of stay for both MSSA and MRSA. Impact on mortality has been variable. Promising novel technologies will not only accurately identify pathogens and detect their resistance markers but will allow discovery of virulence determinants that might further affect patient management.
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Affiliation(s)
- Masako Mizusawa
- Section of Infectious Diseases, Department of Internal Medicine, University of Missouri , Kansas, MO, USA
| | - Karen C Carroll
- Department of Pathology, Division of Medical Microbiology, The Johns Hopkins University School of Medicine , Baltimore, MD, USA
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Kittl S, Brodard I, Heim D, Andina-Pfister P, Overesch G. Methicillin-Resistant Staphylococcus aureus Strains in Swiss Pigs and Their Relation to Isolates from Farmers and Veterinarians. Appl Environ Microbiol 2020; 86:e01865-19. [PMID: 31836575 PMCID: PMC7028968 DOI: 10.1128/aem.01865-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 12/04/2019] [Indexed: 02/06/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) has emerged over the last few decades as a One Health problem with an increasing prevalence in various animal species. The most notable animals are pigs, as asymptomatic carriers, and horses, where there is often an association with infections. The current study looked at the course of MRSA prevalence in Swiss livestock since 2009, with a special focus on pigs, followed by screening of veterinarians and farmers. Livestock isolates were obtained from the Swiss monitoring program and then characterized by spa typing. Concentrating on the year 2017, we analyzed the prevalence of MRSA in Swiss veterinarians and farmers, followed by whole-genome sequencing of selected human and animal strains. The phylogeny was assessed by applying core-genome multilocus sequence typing (MLST) and single-nucleotide polymorphism (SNP) analyses, followed by screening for resistance genes and virulence factors. The prevalence of MRSA in Swiss pigs showed a dramatic increase from 2% in 2009 to 44% in 2017. Isolates typically belonged to clonal complex 398 (CC398), split between spa t011 and t034. The higher prevalence was mainly due to an increase in t011. spa t034 strains from farmers were found to be closely associated with porcine t034 strains. The same could be shown for spa t011 strains from horses and veterinarians. spa t034 strains had a high number of additional resistance genes, and two strains had acquired the immune evasion cluster. However, all but one of the pig spa t011 strains clustered in a separate group. Thus, the increase in pig spa t011 strains does not directly translate to humans.IMPORTANCE MRSA is an important human pathogen; thus, its increasing prevalence in livestock over the last decade has a potentially large impact on public health. Farmers and veterinarians are especially at risk due to their close contact with animals. Our work demonstrates a dramatic increase in MRSA prevalence in Swiss pigs, from 2% in 2009 to 44% in 2017. Whole-genome sequencing allowed us to show a close association between farmer and pig strains as well as veterinarian and horse strains, indicating that the respective animals are a likely source of human colonization. Furthermore, we could demonstrate that pig spa t011 strains cluster separately and are probably less likely to colonize humans than are pig spa t034 strains. This research may provide a basis for a more substantiated risk assessment and preventive measures.
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Affiliation(s)
- Sonja Kittl
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Isabelle Brodard
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Dagmar Heim
- Federal Food Safety and Veterinary Office, Bern, Switzerland
| | | | - Gudrun Overesch
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
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Molecular analysis and epidemiological typing of Vancomycin-resistant Enterococcus outbreak strains. Sci Rep 2019; 9:11917. [PMID: 31417140 PMCID: PMC6695431 DOI: 10.1038/s41598-019-48436-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 08/05/2019] [Indexed: 12/14/2022] Open
Abstract
Outbreaks of multidrug resistant bacteria including vancomycin-resistant enterococci (VRE) in healthcare institutions are increasing in Norway, despite a low level of resistance compared to other European countries. In this study, we describe epidemiological relatedness of vancomycin-resistant Enterococcus faecium isolated during an outbreak at a Norwegian hospital in 2012–2013. During the outbreak, 9454 fecal samples were screened for VRE by culture and/or PCR. Isolates from 86 patients carrying the vanA resistance gene were characterized using pulsed-field gel electrophoresis (PFGE), MALDI-TOF mass spectrometry and single nucleotide polymorphism typing. PFGE revealed two main clusters, the first comprised 56 isolates related to an initial outbreak strain, and the second comprised 21 isolates originating from a later introduced strain, together causing two partly overlapping outbreaks. Nine isolates, including the index case were not related to the two outbreak clusters. In conclusion, the epidemiological analyses show that the outbreak was discovered by coincidence, and that infection control measures were successful. All typing methods identified the two outbreak clusters, and the experiment congruence between the MALDI-TOF and the PFGE clustering was 63.2%, with a strong correlation (r = 72.4%). Despite lower resolution compared to PFGE, MALDI-TOF may provide an efficient mean for real-time monitoring spread of infection.
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