CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database

The Comprehensive Antibiotic Resistance Database (CARD; card.mcmaster.ca) combines the Antibiotic Resistance Ontology (ARO) with curated AMR gene (ARG) sequences and resistance-conferring mutations to provide an informatics framework for annotation and interpretation of resistomes. As of version 3.2.4, CARD encompasses 6627 ontology terms, 5010 reference sequences, 1933 mutations, 3004 publications, and 5057 AMR detection models that can be used by the accompanying Resistance Gene Identifier (RGI) software to annotate genomic or metagenomic sequences. Focused curation enhancements since 2020 include expanded β-lactamase curation, incorporation of likelihood-based AMR mutations for Mycobacterium tuberculosis, addition of disinfectants and antiseptics plus their associated ARGs, and systematic curation of resistance-modifying agents. This expanded curation includes 180 new AMR gene families, 15 new drug classes, 1 new resistance mechanism, and two new ontological relationships: evolutionary_variant_of and is_small_molecule_inhibitor. In silico prediction of resistomes and prevalence statistics of ARGs has been expanded to 377 pathogens, 21,079 chromosomes, 2,662 genomic islands, 41,828 plasmids and 155,606 whole-genome shotgun assemblies, resulting in collation of 322,710 unique ARG allele sequences. New features include the CARD:Live collection of community submitted isolate resistome data and the introduction of standardized 15 character CARD Short Names for ARGs to support machine learning efforts.

Protective effects of alpha-tocopherol and mannitol in both circulatory shock and cerebral ischaemia injury in rat heatstroke

1. There is evidence that hydroxyl radicals are accumulated and oxidative stress is produced in multiple organs, including the brain, of rats with heat stroke. Herein, we investigated the effect on heat stroke-induced circulatory shock and cerebral ischaemic injury of two free radical scavengers, namely mannitol and alpha-tocopherol. 2. Urethane-anaesthetized rats were exposed to heat stress (ambient temperature 42 degrees C) to induce heat stroke. Control rats were exposed to 24 degrees C. Mean arterial pressure and cerebral blood flow after the onset of heat stroke were significantly lower in heat stroke rats than in control rats. However, cerebral free radicals, lipid peroxidation and the neuronal damage score were greater in heat stroke rats compared with control rats. Similarly, plasma cytokines, including tumour necrosis factor-alpha, interleukin (IL)-1beta and IL-6, were significantly higher in heat stroke rats compared with their normothermic controls. 3. Pretreatment with alpha-tocopherol (20 mg/kg, i.v.) or mannitol (10%, i.v.) 30 min before the onset of heat exposure significantly attenuated heat stroke-induced arterial hypotension, cerebral ischaemia and neuronal damage, the increased free radical formation and lipid peroxidation in the brain and the increased plasma levels of cytokines. Pretreatment with alpha-tocopherol or mannitol resulted in a prolongation of survival time in heat stroke. 4. These results demonstrate that although pretreatment with alpha-tocopherol and mannitol does not prevent the heat stroke syndrome entirely, an attenuation of the syndrome is observed.

Hyperbaric oxygen therapy for treatment of postischemic stroke in adult rats

The efficacy of hyperbaric oxygen (HBO) therapy for treatment of stroke remains to be validated in the laboratory. We report here that adult rats subjected to occlusion of the middle cerebral artery and subsequently exposed to HBO (3 atm, 2 x 90 min at a 24-h intervals; animals terminated shortly after the second treatment) or hyperbaric pressure (HBP; 3 atm, 2 x 90 min at a 24-h interval; animals terminated shortly after the second treatment) immediately after the ischemia or after a 60-min delay generally displayed recovery from motor deficits at 2.5 and 24 h of reperfusion, as well as a reduction in cerebral infarction at 24 h of reperfusion compared to ischemic animals subjected to normal atmospheric pressure. While both HBO and HBP treatments promoted beneficial effects, HBO produced more consistent protection than HBP. Treatment with HBO immediately or 60 min after reperfusion equally produced significant attenuations of cerebral infarction and motor deficits. In contrast, protective effects of HBP treatment against ischemia were noted only when administered immediately after ischemia, which resulted in a significantly reduced infarction volume, but only produced a trend toward decreased behavioral deficits. The present results demonstrate that HBO and, to some extent, HBP reduced ischemic brain damage and behavioral dysfunctions.

Diving pattern and work schedule of construction well divers in Taiwan

Construction well divers in Taiwan reportedly suffer a high prevalence of dysbaric osteonecrosis. We studied five divers working at the same construction site. We recorded their diving methods, diving depths, bottom times, work patterns, water temperatures, and heart rates. We also monitored gas bubbles in the subclavian vein in selected dives. A crude but effective hot-water system protected divers against hypothermia and allowed them to work in 24 degrees-27 degrees C water. Divers worked approximately 6.6 h a day and progressed approximately 3.0 m a day while excavating an average of 148 buckets of sand and rock each weighing 49.5 kg. The divers sustained a heart rate increase of 49%. Sixty percent of their equivalent single dive bottom times exceeded the U.S. Navy's no-decompression limits. Two cases of venous bubbles were detected, and one of these divers showed symptoms of decompression sickness. The prolonged bottom time and lack of a decompression schedule probably contributed to a risk of decompression sickness and dysbaric osteonecrosis.

Diving pattern of fishermen in the Pescadores

Professional diving fishermen in the Pescadores Archipelago (119.30 degrees W, 23.30 degrees N) dive with a simple hookah system. Although they use modern equipment, such as wet suit, face mask, mouth piece with demand valve, spear gun, weight belt, and fins, their lack of knowledge of diving medicine is apparent. On the average, 180 cases of decompression sickness (DCS) per year were reported to occur in the Pescadores. We conducted studies in 1990 and 1992 on three islands of the Archipelago. At the time of our study, an estimated 140 diving fishermen resided on these three islands. Of the 62 fishermen interviewed, 14 volunteered for the recording of dive profiles using a diver-carried data logger. In the summer of 1990, a group of eight fishermen dived, on the average, to a depth of 17.8 +/- 5.3 m (mean +/- SD; range, 8-27 m) for 26.9 +/- 19.7 min (5-66 min). Although the diving depth was similar to that of the average recollections of 43 divers, 20.1 +/- 4.4 m (15-30 m), the actual diving time was far shorter than that of their recollections, 426 +/- 138 min (240-630 min). The post-typhoon sea floor conditions may have shortened their diving time. In the summer of 1992, a group of six fishermen dived to 20.5 +/- 3.8 m (15-26 m) for 56.4 +/- 21.2 min (18-84 min). Again, the diving depth matched that of their recollection well, 22.2 +/- 2.5 m (20-26 m), but their bottom time was far shorter than they believed, 270 +/- 108 min (120-480 min). They used no decompression procedures, regardless of the bottom time and diving depth. In the 1990 group, 5 out of 10 equivalent single dive bottom times (ESDBT) exceeded U.S. Navy no-decompression (No-D) air dive limits; whereas in the 1992 group, 7 out of 9 ESDBTs exceeded No-D limits. Eight of the 38 discrete dives exceeded the No-D limits, even if we underestimate their decompression stress by disregarding their repetitive dive history. However, no symptoms of DCS were observed in either the 1990 or 1992 groups of 14 divers, despite 63% of the ESDBTs and 21% of discrete dives having exceeded the No-D limits. Adaptation to diving work may have allowed them to exceed the established No-D limits. The existing records of incidence of DCS from this region suggest that previously they must have dived longer or deeper or both during times of abundant resources.

Hyperbaric oxygen therapy in clinical application. A report of a 12-year experience

Hyperbaric oxygen (HBO) has become a useful treatment in clinical diseases. All the treatment profiles (Death/Time) were performed under the safe limit of unit pulmonary toxicity dose (UPTD). Between June 1976 and December 1987, we had treated 1288 cases with HBO. The effective rates (cure or improvement) were 97.5% for decompression sickness, 96.3% for chronic osteomylitis, 90% for chronic skin ulcer, 89.4% for crush injury, 81.3% for gas intoxication, 76.1% for burn injury, 73.3% for cerebrovascular accident, 57.1% for gas gangrene, 50% for retinal artery insufficiency, and 45.5% for head or spinal cord injury. Only 3 patients suffered from oxygen toxicity and relieved immediately. To the serious decompression sickness, the comparative study between the conventional treatment table and our modified table revealed increased cure rate(25.8% versus 50.0%, P less than 0.05), and decreased recurrence rate (16.1% versus 4.1%, P less than 0.05). In burn patients with 35-70% area involved and 15-45 years of age, the comparative analysis showed a reduced mortality rate of 6.8% for the HBO treated group as opposed to 14.8% for the non-HBO treated group, P less than 0.05.