Table 1.
Summary of study characteristics of the 38 included studies
| First Author | Location | Hospital setting | Study type | Microbiological detection and/or identification | Antimicrobial susceptibility testing method |
|---|---|---|---|---|---|
| Chowdhary [31] | New Delhi, India | ICU | Retro-spective Cohort | MALDI-ToF MS | CLSI Broth Microdilution Method M27-A3/S4 |
| Bogossian [44] | Brussels, Belgium | ICU | Retro-spective Case Control | Routine surveillance swabs: chromID® CARBA SMART agar, MacConkey agar containing ceftazidime chromID® VRE agar, MALDI-ToF MS |
EUCAST: VITEK 2 and disk diffusion Carbapenemases OXA-48, KPC, NDM, VIM and IMP; VanA, VanB were detected via PCR analysis or Coris Resist-5 O.O.K.N.V. antigenic. MDR Pseudomonas spp. and Acinetobacter spp. were defined as recommended considering antimicrobial resistance phenotype |
| Ramadan [33] | Assiut, Egypt | Tertiary hospitals: Alrahji Liver Hospital and Assiut University Hospital | Prospective Cohort | MALDI-ToF MS | Detection of antibiotic resistance genes by Monoplex PCR Technique (mecA, NDM-1, KPC, TEM, CTX-M, SHV) |
| Amarsy [45] | Nantes, France | ICU | Retro-spective Cohort | Blood cultures and respiratory cultures | Detection of resistance genes by Illumina WGS |
| Perez [19] | New Jersey, USA | ICU, Medical-surgical unit, progressive care unit | Retro-spective Cohort | Clinical specimens, colonization screening |
CRAB definition: Detection using RT-PCR for carbapenemase genes |
| Salehi [22] | Tehran, Iran | Three tertiary care training hospitals | Cross-Sectional | Budding yeasts and pseudohyphae in KOH 10% preparation and culture | CLSI M60 and M59 supplements |
| Cataldo [46] | Rome, Italy | ICU | Retro-spective Cohort | Blood cultures | NA |
| Posteraro [47] | Basel, Switzerland | COVID care unit | Case Report | MALDI-ToF MS | Sensititre YeastOne® method confirmed by the CLSI M27-A3 reference method |
| Nori [3] | New York, City, NY, USA | ICU | Retro-spective Observa-tional | Respiratory cultures, blood cultures | NA |
| Mahmoudi [48] | Hamedan, Iran | Nahavand Hospitals | Cross-Sectional | Blood and endotracheal aspirate samples | CLSI |
| Li [22] | Wuhan, China | Hospital (designated for COVID patients) | Retro-spective Cross-Sectional | Qualified sputum, endotracheal aspirate, bronchoalveolar lavage fluid, blood samples, or qualified urine | CLSI |
| Contou [18] | Argenteuil, France | COVID ICU | Retro-spective Cross-Sectional | Blood cultures, cultures of the respiratory tract secretions | Panel RP2 plus (Film Array Biomerieux®), Panel Pneumonia Plus (Film Array Biomerieux®) |
| Mo [22] | Brooklyn, New York | Community Teaching Hospital | Case Series (Retro-spective Observa-tional) | NA | NA |
| Garcia-Menino [8] | Oviedo, Spain | ICU | Case Series (Retro-spective Observa-tional) | MALDI TOF/MS - | Microscan System (BeckmanCoulter, Brea, CA, USA); results interpreted according to EUCAST |
| Sharifipour [20] | Qom, Iran, | ICU | Prospective Cohort | Samples were cultured on Blood Agar, Chocolate Agar, Eosin Methylene Blue (EMB), and MacConkey Agar | CLSI |
| Walpole [50] | United Kingdom | ICU | Case Report | Sputum sample | NA |
| Razazi [10] | France | ICU | Retro-spective Cohort | Bacterial co-infection at ICU admission evidenced by detection of bacteria in sputum or blood samples, in the absence of other sources of infection, or by a positive pneumococcal or L. pneumophila serotype 1 urinary antigen test | Susceptibility profiles of recovered microorganisms were recorded |
| Guisado-Gil [17] | Seville, Spain | ICU | Retro-spective Cohort | Blood cultures obtained > 48 h after admission | EUCAST. MDR categorization according to the Germany Society for Hygiene and Microbiology |
| Montrucchio [51] | Turin, Italy | ICU | Case Series (Retro-spective Observa-tional) | MALDI-ToF MS | EUCAST: Microscan WalkAway plus System, MASTDISCS® Combi Carba plus disk system |
| Mady [23] | Riyadh, Saudi Arabia | ICU | Case Series (Retro-spective Observa-tional) | Blood and respiratory cultures | Not described |
| Tiri [52] | Terni, Italy | ICU | Retro-spective Observa-tional Cohort | MALDI-ToF MS | VITEK2; Immunochromatography for OXA-48-like, OXA-163, KPC, NDM, VIM |
| Kokkoris [53] | Athens, Greece | ICU | Case Series (Retro-spective Observatio-nal Cohort) | Blood specimen | NA |
| Perrotta [54] | FG, Italy | ICU | Case Report | NA | NA |
| Baiou [55] | Doha, Qatar | ICU | Retro-spective Case–Control | MALDI-ToF MS | BD Phoenix according to CLSI standards |
| Segrelles-Calvo [56] | Madrid, Spain | ICU, RICU | Prospective Observa-tional Cohort | Aspergillus galactomannan antigen on BAL | Not described |
| Martinez-Guerra [57] | Mexico City, Mexico | COVID-19 dedicated facility | Prospective Cohort | MALDI-Tof MS | VITEK2; AmpC producers considered with known chromosomal AmpC Beta-Lactamases, ESBL considered in those resistant to 3rd generation cephalosporins and monobactams, CRE considered with resistance to carbapenems in VITEK and confirmed with modified CIM test, MDR P. aeruginosa considered in isolates with resistance to at least one agent in three or more antibiotic categories |
| Karruli [58] | Naples, Italy | ICU | Retro-spective Observa-tional Cohort | Microbiological sampling of blood, urine, and airways | MDR defined according to Magiorakos et al. [59] criteria |
| Gomez-Simmonds [60] | New York City, USA | ICU | Retro-spective Observational Cohort | Surveillance using MicroScan | Xpert Carba-R, BMD, E-test, WGS |
| Cultrera [61] | Ferrara, Italy | ICU | Retro-spective Observational Cohort | MALDI-ToF MS | VITEK2 |
| Khurana [62] | New Delhi, India | COVID-19 dedicated facility | Retro-spective Observational Cohort | VITEK2 and BioFire FilmArray Respiratory Panel | VITEK2 AST card interpreted by CLSI guidelines |
| Posteraro [47] | Rome, Italy | ICU | Retro-spective Observa-tional Cohort | Positive blood culture using BacT/ALERT VIRTUO and MALDI Biotyper | VITEK2 and Sensititre YeastOne® following EUCAST breakpoints |
| Pascale [63] | Bologna, Italy | ICU and non-ICU settings | Cross-Sectional | Active surveillance of blood and respiratory cultures | CRE defined as per EUCAST criteria; WGS |
| Baskaran [64] | England | ICU | Multicentre Retro–spective Observa-tional Cohort | Standard culture, respiratory viral PCR and urinary antigen tests | NA |
| Moretti [65] | Brussels, Belgium | ICU | Retro-spective Observational Cohort | Endotracheal aspiration or BAL with > 105 and > 104 CFU/mL | Not described. MDR or extreme-drug resistant (XDR) based on European Center of Disease Prevention and Control (ECDC) |
| Grasselli [66] | Genoa, Italy | ICU | Retro-spective Observa-tional Cohort | Routine microbiological surveillance: perineal swabs, nasal swabs, tracheal aspirate, urine culture | Not described |
| Magnasco [67] | Genoa, Italy | ICU | Retro-spective Observa-tional Cross-Sectional | Blood, respiratory and urinary samples using VITEK MS | VITEK2; Sensititre YeastOne® Panel (antifungal) |
| Bentivegna [68] | Rome, Italy | COVID-19 Depart-ment | Case–Control | NA | NA |
| Suarez-de-la-Rica [69] | Madrid, Spain | CCU | Retro-spective Observational Cohort | Conventional culture | Not described |
Abbreviations: Bronchoalveolar Lavage (BAL), Clinical and Laboratory Standards Institute (CLSI), Critical Care Unit (CCU), European Committee on Antimicrobial Susceptibility Testing (EUCAST), intensive care unit (ICU), multi-drug resistant (MDR), matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), polymerase chain reaction (PCR), whole-genome sequencing (WGS), carbapenem resistant Acinetobacter baumannii (CRAB), respiratory intensive care unit (RICU), real-time polymerase chain reaction (RT-PCR), oropharyngeal candidiasis (OPC)