Genetic diversity and comparison of diagnostic tests for characterization of foot-and-mouth disease virus strains from Pakistan 2008-2012

We report the laboratory analysis of 125 clinical samples from suspected cases of foot-and-mouth disease (FMD) in cattle and Asian buffalo collected in Pakistan between 2008 and 2012. Of these samples, 89 were found to contain viral RNA by rRT-PCR, of which 88 were also found to contain infectious FMD virus (FMDV) by virus isolation (VI), with strong correlation between these tests (κ = 0.96). Samples that were VI-positive were serotyped by antigen detection ELISA (Ag-ELISA) and VP1 sequence acquisition and analysis. Sequence data identified FMDV serotypes A (n = 13), O (n = 36) and Asia-1 (n = 41), including three samples from which both serotypes Asia-1 and O were detected. Serotype A viruses were classified within three different Iran-05 sublineages: HER-10, FAR-11 and ESF-10. All serotype Asia-1 were within Group VII (Sindh-08 lineage), in a genetic clade that differs from viruses isolated prior to 2010. All serotypes O were classified as PanAsia-2 within two different sublineages: ANT-10 and BAL-09. Using VP1 sequencing as the gold standard for serotype determination, the overall sensitivity of Ag-ELISA to correctly determine serotype was 74%, and serotype-specific sensitivity was 8% for serotype A, 88% for Asia-1 and 89% for O. Serotype-specific specificity was 100% for serotype A, 93% for Asia-1 and 94% for O. Interestingly, 12 of 13 serotype A viruses were not detected by Ag-ELISA. This study confirms earlier accounts of regional genetic diversity of FMDV in Pakistan and highlights the importance of continued validation of diagnostic tests for rapidly evolving pathogens such as FMDV.

Sampling variability in the microbiological evaluation of expectorated sputa and endotracheal aspirates

A five-center study was conducted with the aim of determining how reproducibly expectorated sputa and tracheal aspirates could be sampled when preparing Gram-stained smears and inoculating cultures. With both specimen types, excessive variation was noted among Gram stain results obtained from replicate smears. Less variation was noted among culture results, especially with tracheal aspirates.

Microdilution antifungal susceptibility testing of Candida albicans and Cryptococcus neoformans with and without agitation: an eight-center collaborative study

The growth patterns observed in the trailing wells when fluconazole is being tested may give rise to readings that suggest resistance or increased MICs for known susceptible strains. We conducted a multicenter study to evaluate the intralaboratory and interlaboratory reproducibilities of a method that uses agitation to disperse these types of growth. Ten strains of Candida albicans and five strains of Cryptococcus neoformans were tested against fluconazole, flucytosine, and amphotericin B by using a microdilution adaptation of the proposed reference method of the National Committee for Clinical Laboratory Standards for yeasts (M27-T). The endpoint criterion used before agitation was consistent with the M27-T recommendation, while a criterion of 50% or more reduction of growth compared with the control was used after agitation. The results of this study showed that use of agitation and the modified endpoint criterion both improved intralaboratory and inter-laboratory agreement and increased the frequency of interpretable MICs. The MICs obtained by this method were comparable to those obtained by the broth macrodilution M27-T method. Like M27-T, this method was not able to definitely distinguish amphotericin B-susceptible from -resistant strains, although the MICs for the resistant strains were consistently higher than those for the susceptible ones. The findings imply that agitation should be seriously considered when antifungal agents, particularly fluconazole, are tested in a microdilution format.

A blocking ELISA for detection of antibody to a subgroup-reactive epitope of African horsesickness viral protein 7 (VP7) using a novel gamma-irradiated antigen

A novel gamma irradiated inactivated cell culture derived African horsesickness viral (AHSV) antigen was used in a blocking ELISA (B-ELISA) for detecting antibody to a subgroup-reactive epitope of AHSV. A monoclonal antibody (MAB), class IgM, against an epitope on African horsesickness (AHS) viral protein 7 (VP7) was developed in BALBc mice and used in the B-ELISA. The MAB, designated F9H, was blocked by 69 serums from equidae with antibody to AHS, but its binding activity was not appreciably affected by 301 serums that did not contain antibodies to AHS virus. An ELISA protocol using a blocking format is described.

Effect of threonine-to-methionine substitution at position 265 on structure and function of TEM-1 beta-lactamase

TEM beta-lactamase variants with the amino acid substitutions R164S, E104K, G238S, and E240K (ABL numbering) display increased activity toward extended-spectrum cephalosporins. The T265M substitution is frequently found to be associated with the above substitutions in extended-spectrum beta-lactamases. However, the residue is located away from the active site in the three-dimensional structure and has been assumed to have no effect on catalysis. To examine the effect of the substitution on the structure and function of TEM beta-lactamase we constructed the following mutants: G238S, T265M, T265M:G238S, and T265M:G238S:E240K. Each enzyme was purified to homogeneity and the kinetic parameters kcat, Km and kcat/Km were determined for cefotaxime, ceftazidime, cephaloridine, and ampicillin. The results indicate that the T265M mutation has little effect on hydrolysis. In addition, we used immunoblotting to show that the substitution has little or no effect on the in vivo steady-state levels of beta-lactamase.

Characterization of TEM-1 beta-lactamase mutants from positions 238 to 241 with increased catalytic efficiency for ceftazidime

Recently, TEM beta-lactamase variants with amino acid substitutions in the active-site pocket of the enzyme have been identified in natural isolates with increased resistance to extended-spectrum cephalosporins such as cefotaxime and ceftazidime. To identify other amino acid substitutions that alter the activity of TEM-1 toward extended-spectrum cephalosporins, a random library was constructed that contained all possible amino acid substitutions over the 3-residue window of 238-241 (ABL numbering). Mutants were selected for 100-fold greater ceftazidime resistance than wild-type. All mutants had a serine substitution at position 238, a lysine or arginine at position 240, and a small amino acid at position 241. The role of each substitution was investigated by constructing individual G238S, E240K, and R241G substitutions as well as the G238S:E240K double mutant. Each enzyme was purified to homogeneity and the kinetic parameters kcat and Km were determined using several substrates. The G238S substitution increases catalytic efficiency for both ceftazidime and cefotaxime. However, to achieve large increases in catalytic efficiency, both G238S and the E240K substitutions are required. The R241G substitution results in a small increase in catalytic efficiency for only ceftazidime. The contribution of each residue to the transition-state stabilization energy was found to be additive indicating that the substitutions act independently to change the catalytic properties of the enzyme.

Evolution of antibiotic resistance: several different amino acid substitutions in an active site loop alter the substrate profile of beta-lactamase

In order to understand how TEM-1 beta-lactamase substrate specificity can be altered by mutation, amino acid residues 161 through to 170 were randomly mutagenized to sample all possible amino acid substitutions. The 161-170 region includes a portion of an omega loop structure, which is involved in the formation of the active-site pocket. The percentage of random sequences that provide bacterial resistance to either ampicillin or to the extended-spectrum cephalosporin ceftazidime was determined. It was found that the sequence requirements for wild-type levels of ampicillin resistance are much more stringent than the sequence requirements for ceftazidime resistance. Surprisingly, more than 50% of all amino acid substitutions in the 161-170 region result in levels of ceftazidime resistance at least three times greater than wild type. In addition, by increasing the level of the selection for ceftazidime resistance, substitutions that result in a greater than 100-fold increase in ceftazidime resistance were identified. Characterization of altered beta-lactamase enzymes indicated that while their catalytic efficiency (kcat/Km) for ceftazidime hydrolysis is higher, the enzymes are poorly expressed relative to wild-type TEM-1 beta-lactamase.

Two-site comparison of broth microdilution and semisolid agar dilution methods for susceptibility testing of Cryptococcus neoformans in three media

This study evaluated the inter- and intralaboratory agreement between results of the semisolid agar dilution and broth microdilution methods of antifungal susceptibility testing of Cryptococcus neoformans. Three media were tested in two laboratories. The drugs tested were amphotericin B, flucytosine, itraconazole, fluconazole, and Schering 39304. Analysis by kappa statistics revealed good agreement between the laboratories for the two methods. The highest level of inter- and intralaboratory agreement was observed in RPMI 1640 with L-glutamine followed by Eagle's minimum essential medium and yeast nitrogen broth. The broth microdilution method appears more suitable than the semisolid agar dilution method for testing cryptococci because of its ease in performance, cost, and simplicity.

Collaborative investigation of broth microdilution and semisolid agar dilution for in vitro susceptibility testing of Candida albicans

A study was performed in two laboratories to evaluate the effect of growth medium and test methodology on inter- and intralaboratory variations in the MICs of amphotericin B (AMB), flucytosine (5FC), fluconazole (FLU), itraconazole (ITRA), and the triazole Sch 39304 (SCH) against 14 isolates of Candida albicans. Testing was performed by broth microdilution and semisolid agar dilution with the following media, buffered to pH 7.0 with morpholinepropanesulfonic acid (MOPS): buffered yeast nitrogen base (BYNB), Eagle's minimal essential medium (EMEM), RPMI 1640 medium (RPMI), and synthetic amino acid medium for fungi (SAAMF). Inocula were standardized spectrophotometrically, and endpoints were defined by the complete absence of growth for AMB and by no more than 25% of the growth in the drug-free control for all other agents. Comparative analyses of median MICs, as determined by each test method, were made for all drug-medium combinations. Both methods yielded similar (+/- 1 twofold dilution) median MICs for AMB in EMEM and RPMI, 5FC in all media, and FLU in EMEM, RPMI, and SAAMF. In contrast, substantial between-method variations in median MICs were seen for AMB in BYNB and SAAMF, FLU In BYNB, and ITRA and SCH in all media. Interlaboratory concordance of median MICs was good for AMB, 5FC, and FLU but poor for ITRA and SCH in all media. Endpoint determinations were analyzed by use of kappa statistical analyses for evaluating the strength of observer agreement. Moderate to almost perfect interlaboratory agreement occurred with AMB and 5FC in all media and with FLU in EMEM, RPMI, and SAAMF, irrespective of the test method. Slight to almost perfect interlaboratory agreement occurred with ITRA and SCH in EMEM, RPMI, and SAAMF when tested by semisolid agar dilution but not broth microdilution. Kappa values assessing intralaboratory agreement between methods were high for 5FC in all media, for AMB in BYNB, ENEM, and RPMI, and for FLU in EMEM, RPMI, and SAAMF. One laboratory, but not the other, reported substantial to almost perfect agreement between methods for ITRA, and SCH in EMEM, RPMI, and SAAMF. Both laboratories reported poor agreement between methods for the azoles in BYNB. Discrepancies noted in azole-BYNB combinations were largely due to the greater inhibitory effect of these agents in BYNB than in other media. These results indicate that the semisolid agar dilution and broth microdilution methods with EMEM or RPMI yield equivalent and reproducible MICs for AMB, 5FC, and FLU but not ITRA and SCH.

Bacterial flora of the gastrointestinal tract of opossums

The bacterial flora of the stomach, small intestine, cecum and bile from 20 healthy opossums (Didelphis virginiana) captured from the wild was studied. Results showed that their gastrointestinal flora was similar to that found in other small mammals but, in addition, opossums are heavily colonized by Salmonella spp., which might adversely affect their adequacy as laboratory animals for some experimental protocols.

The effect of postnatal age on the adherence of enterohemorrhagic Escherichia coli to rabbit intestinal cells

Enterohemorrhagic Escherichia coli (EHEC) are associated with hemorrhagic colitis and hemolytic uremic syndrome. These illnesses are typically seen in young children, but are rare before 6 mo of age. The cause of this age restriction is unclear. Because bacterial adherence to intestinal mucosa is considered a critical initial event in pathogenesis, we studied the ontogeny of the adherence of EHEC (O157:H7 and other serotypes) isolated from children with diarrhea, hemorrhagic colitis, or hemolytic uremic syndrome. Adherence was quantitatively determined by incubating radiolabeled bacteria with viable rabbit intestinal cells, which were prepared by treating loops of distal ileum and proximal colon with EDTA, DTT, and citrate. Cells obtained from animals of different ages were studied simultaneously. The adherence of the various EHEC strains varied significantly. A non-O157:H7 E. coli strain 43-12 bound best (35 and 32 bacteria/cell to ileal and colonic cells, respectively) with 48-60% inhibition by D-mannose and alpha-methyl mannoside (p less than 0.01) and 20-28% inhibition by L-fucose (p less than 0.05), but no significant inhibition by other carbohydrates. Analysis of variance and polynomial regression showed that postnatal age significantly affected the adherence to ileal and colonic cells. Adherence during the 1st wk of life was 13-19% of that in the adult animal; it increased gradually, reaching the adult level at about 4 wk of age. Our study shows that postnatal age affects the adherence of EHEC to intestinal cells. These findings are compatible with postnatal development of gut receptors and may be relevant to the age-related risk of EHEC disease in children.

Antimicrobial susceptibility of clinical isolates of Haemophilus influenzae to ampicillin-sulbactam

A total of 1092 clinical isolates of Haemophilus influenzae (306 type b; 786 non-type-b), from five medical centers were obtained during 1987 and 1988. Disk diffusion antimicrobial susceptibilities were obtained for all isolates, and broth microdilution susceptibilities were obtained for 502 isolates. Beta-lactamase was produced by 34.3% of type-b and 22.1% of non-type-b isolates, with some geographic variations. Using disk diffusion antimicrobial susceptibility testing, all isolates were susceptible to ampicillin-sulbactam, ceftriaxone, cefuroxime, and rifampin; two isolates were resistant to chloramphenicol. Whether tested using a fixed ratio of ampicillin to sulbactam of 2:1 or a fixed concentration of sulbactam, the ampicillin-sulbactam combination demonstrated good activity against clinical isolates of H. influenzae. Only 8 of the 1092 isolates did not produce beta-lactamase but demonstrated MICs of greater than or equal to 2 micrograms/ml for ampicillin.

Evaluation of computer case simulations for teaching clinical pathology to second-year medical students

A computer-assisted learning program for teaching clinical pathology to second year medical students has been developed and evaluated. These programs are designed to be used as supplements to formal lectures, laboratory exercises, and small group discussions. Students are given case histories and asked to select differential diagnoses, order and interpret laboratory and diagnostic tests, and make final diagnostic conclusions. In some cases, laboratory monitoring of treatment, e.g., drug therapy, is emphasized. The performance of the student is objectively evaluated during each stage. In addition, the amount spent for each workup is recorded with penalties given for excess or inappropriate test ordering. Separate evaluations are performed to assess the effectiveness of these programs as an alternative teaching format to (1) formal lectures and reading assignments, and (2) faculty-directed small group discussions. It is concluded that the computer-assisted learning method is equivalent to lectures and group discussions and is a format that is well accepted by students.

Comparative in vitro activity of ceftibuten (Sch 39720) against bacterial enteropathogens

Ceftibuten is a new orally active cephalosporin with significant bioavailability. Its in vitro activity was compared with those of other agents against 383 strains of enteric pathogens derived from clinical specimens. Ceftibuten was very active against the strains of the family Enterobacteriaceae tested (overall MIC for 90% of strains tested, 0.25 microgram/ml) but was less active against Campylobacter jejuni (MIC for 90% of strains, 16 micrograms/ml). The MBC was one to two dilutions higher than the corresponding MICs for most pathogens tested.

Reactivity of serologic tests for the detection of antibody specific to cytomegalovirus. II. Latex agglutination and enzyme-linked immunosorbent assay

Two hundred seven sera were assayed for antibody-specific for cytomegalovirus (CMV) by two enzyme immunoassays (EIAs; Bioenzabody, Litton Bionetics, and Abbott CMV Total Antibody EIA, Abbott Laboratories) and latex agglutination (LA; CMVScan, Hynson, Westcott and Dunning). The overall accuracy of the LA, Litton EIA, and Abbott EIA was 95.8%, 86.2%, and 88.6%, respectively. Although the Abbott EIA had a sensitivity of 98.8%, the specificity was only 35.5%. The positive predictive values of the LA, Litton EIA, and Abbott EIA were 99.4%, 95.9%, and 88.9%, respectively, while the negative predictive values of each of these tests were 81.1%, 56.2%, and 84.6%, respectively.