Image analysis and artificial intelligence in infectious disease diagnostics.

BACKGROUND: Microbiologists are valued for their time-honed skills in image analysis, including identification of pathogens and inflammatory context in Gram stains, ova and parasite preparations, blood smears and histopathologic slides. They also must classify colony growth on a variety of agar plates for triage and assessment. Recent advances in image analysis, in particular application of artificial intelligence (AI), have the potential to automate these processes and support more timely and accurate diagnoses. OBJECTIVES: To review current AI-based image analysis as applied to clinical microbiology; and to discuss future trends in the field. SOURCES: Material sourced for this review included peer-reviewed literature annotated in the PubMed or Google Scholar databases and preprint articles from bioRxiv. Articles describing use of AI for analysis of images used in infectious disease diagnostics were reviewed. CONTENT: We describe application of machine learning towards analysis of different types of microbiologic image data. Specifically, we outline progress in smear and plate interpretation as well as the potential for AI diagnostic applications in the clinical microbiology laboratory. IMPLICATIONS: Combined with automation, we predict that AI algorithms will be used in the future to prescreen and preclassify image data, thereby increasing productivity and enabling more accurate diagnoses through collaboration between the AI and the microbiologist. Once developed, image-based AI analysis is inexpensive and amenable to local and remote diagnostic use.

Continuous positive airway pressure-associated cutaneous amoebiasis in an immunosuppressed patient.

Organisms of the genus Acanthamoeba are environmentally ubiquitous and colonizers of the oral mucosa in humans. While largely asymptomatic in healthy persons, Acanthamoeba infection can cause disseminated disease with poor prognosis in immunosuppressed populations. Here we report a unique case of cutaneous amoebiasis associated with continuous positive airway pressure use in an immunosuppressed patient.

Evidence for pore-forming ability by Legionella pneumophila.

Legionella pneumophila is the cause of Legionnaires' pneumonia. After Internalization by macrophages, it bypasses the normal endocytic pathway and occupies a replicative phagosome bound by endoplasmic reticulum. Here, we show that lysis of macrophages and red blood cells by L. pneumophila was dependent on dotA and other loci known to be required for proper targeting of the phagosome and replication within the host cell. Cytotoxicity occurred rapidly during a high-multiplicity infection, required close association of the bacteria with the eukaryotic cell and was a form of necrotic cell death accompanied by osmotic lysis. The differential cytoprotective ability of high-molecular-weight polyethylene glycols suggested that osmotic lysis resulted from insertion of a pore less than 3 nm in diameter into the plasma membrane. Results concerning the uptake of membrane-impermeant fluorescent compounds of various sizes are consistent with the osmoprotection analysis. Therefore, kinetic and genetic evidence suggested that the apparent ability of L. pneumophila to insert a pore into eukaryotic membranes on initial contact may play a role in altering endocytic trafficking events within the host cell and in the establishment of a replicative vacuole.

The nature and extent of training activities in clinical pathology required for effective consultation on laboratory test selection and interpretation.

OBJECTIVE: The goal of this study was to identify the activities in clinical pathology training and the length of time required in each to effectively train residents as consultants on laboratory test selection and interpretation. METHODS: The information needed to address these questions was obtained from a study of 20 residents in clinical pathology at our institution between 1990 and 1996. In the survey participants were asked to assess the value of specific training activities in developing their confidence when addressing consultative questions on laboratory test use and interpretation. Participants were also asked to assess the length of time required to gain confidence in performing this role. RESULTS: The results of the study demonstrate that confidence in providing advice on clinical laboratory test selection and interpretation is acquired to a significant but not absolute degree after an intense 8-week experience in a single clinical laboratory subspecialty, during which time no other responsibilities are assigned. The data also indicate that interactions with clinical pathologists and formal lectures provided to the trainees during their rotations are critical components of the consultation service. There was a significant decrease in the length of time required to provide effective information on test selection and interpretation as the residents progressed through their training. CONCLUSIONS: For all of the major subspecialties in clinical pathology, the residents gained significant confidence by 4 weeks of intense training, and by 8 weeks participants were very confident in answering consultation questions. Even after 8 weeks, however, fewer than 10% of the residents felt absolutely confident in their own decisions regarding laboratory test use and interpretation prior to discussion with senior residents and faculty. Thus, acquisition of expertise to effectively provide advice on laboratory test selection and interpretation required up to 8 weeks of focused training in each clinical laboratory subspecialty. Gaining confidence in multiple areas requires a significant commitment of full-time training. This study provides an understanding of the type and extent of training required to attain the skills necessary to effectively provide consultation in clinical pathology.

Excision of a P4-like cryptic prophage leads to Alp protease expression in Escherichia coli.

The Escherichia coli K-12 alpA gene product, when overproduced from a multicopy plasmid, leads to suppression of the capsule overproduction and UV sensitivity phenotypes of cells mutant for the Lon ATP-dependent protease. This suppression has previously been shown to correlate with increased in vivo activity of a previously unknown energy-dependent proteolytic activity capable of degrading Lon substrates, the Alp protease. We show in an accompanying paper that alpA, which has homology to a short open reading frame in bacteriophage P4, acts as a positive transcriptional regulator of slpA, a gene linked to alpA and necessary for suppression of lon mutants (J. E. Trempy, J. E. Kirby, and S. Gottesman, J. Bacteriol. 176:2061-2067). The sequence of slpA suggests that it encodes an integrase gene closely related to P4 int and that both alpA and slpA are part of a cryptic P4-like prophage. AlpA expression increases SlpA synthesis. Increased SlpA leads, in turn, to the excision and loss of the cryptic prophage. Excision is dependent on integration host factor as well as on SlpA. Prophage excision is necessary but not sufficient for full expression of the Alp protease. A second function (named AHA) allows full protease expression; this function can be provided by the kanamycin resistance element from Tn903 when the element is present on a multicopy plasmid. Excision and loss of the cryptic prophage apparently allow expression of the Alp protease by inactivating a small stable RNA (10Sa RNA) encoded by the ssrA gene. The precursor of this RNA has its 3' end within the cryptic prophage; the mature 3' end lies within the prophage attL site. Inactivation of ssrA by insertional mutagenesis is sufficient to allow expression of the suppressing Alp protease, even in the presence of the cryptic prophage. Therefore, 10Sa RNA acts as a negative regulator of protease synthesis or activity, and prophage excision must inactivate this inhibitory function of the RNA.

Alp suppression of Lon: dependence on the slpA gene.

We have previously found that plasmids carrying the Escherichia coli alp gene (now to be called alpA) suppress two phenotypes of a delta lon protease mutant, overproduction of capsular polysaccharide and sensitivity to UV light. Suppression of these lon phenotypes is most likely explained by the increased degradation of the Lon substrates responsible for these phenotypes. We have called this suppressing protease activity Alp protease. The Alp protease activity is detected in cells after introduction of plasmids carrying the alpA gene, which encodes an open reading frame of 70 amino acids. Insertions which abolish Alp activity interrupt this open reading frame. We have used Tn10 and lambda placMu mutagenesis to identify a chromosomal locus, slpA, that is required for alpA+ suppression of delta lon. This locus maps at 57 min, close to the chromosomal location of alpA. The expression of beta-galactosidase from a lac transcriptional fusion to slpA is increased six- to eightfold when the alpA+ gene is present on a multicopy plasmid. Therefore, AlpA acts as a transcriptional regulator of the slpA gene(s); activation of slpA transcription is necessary to suppress the phenotypes of a delta lon mutation. In an accompanying paper (J. E. Kirby, J. E. Trempy, and S. Gottesman, J. Bacteriol. 176:2068-2081, 1994), we show that neither AlpA nor SlpA is a component of the protease itself but that they are part of a regulatory cascade which leads to expression of the Alp protease.

Effect of intravenous infusion of atriopeptin 3 on immediate renal allograft function.

Thirty-eight recipients of nineteen pairs of cadaveric kidneys were entered into a double-blind randomized study in which one recipient received a 12-hour intravenous infusion of Atriopeptin III (AP-3), a synthetic analogue of atrial natriuretic factor, commencing at release of the vascular clamps, and the other received a placebo infusion. In an initial dose ranging study, successive groups of six kidneys (3 pairs) were randomized to receive each of 0.0125, 0.025, 0.05 micrograms/kg/min AP-3 or placebo. Thereafter 20 kidneys (10 pairs) received 0.1 micrograms/kg/min or placebo. There was no discernable effect of AP-3 on allograft creatinine clearance or sodium excretion either when the highest dose of AP-3 was considered alone or when all doses were considered together. Averaged creatinine clearance over the period 0 to 24 hours after transplantation was 20.1 +/- 14.7 ml/min in patients receiving active treatment and 18.2 +/- 13.7 ml/min in those receiving placebo. Thus, despite the documentation of a protective effect of atrial natriuretic factor in animal models of renal ischemia, it is unlikely that intravenous infusion of AP-3 in this dose range will be of benefit in improving immediate renal allograft graft function.

Microwave disinfection of soft contact lenses.

We evaluated the effectiveness and convenience of microwave irradiation as a method of disinfecting soft contact lenses. Soft contact lenses from each of the four Food and Drug Administration (FDA) categories were placed in sterile vials and immersed in 2 ml of saline which had been contaminated with one of three common species of bacteria. The contaminated lens vials were placed in a standard 600 W microwave oven and exposed to microwave irradiation times ranging from 30 to 180 s. Significant reductions in bacteria colony counts were found after 30 s of microwave irradiation. Few of the bacteria survived 60 s of microwave exposure and none survived 90 s. Our findings indicate that microwave disinfection can be an effective and rapid means of killing bacteria on soft lenses and in the storage solution. However, further studies are necessary to determine the minimum exposure time required, the effect of microwave disinfection on other microorganisms, and the effect of microwave irradiation on contact lens polymers and lens dimensions.