Sources of bacterial strains.

<p>Sources of bacterial strains.</p

Zones of inhibition (mm) as measured by disk diffusion and interpretation of resistance phenotype¹^,²^,³.

<p>Tests were performed in duplicate, and both measurements are reported for each organism/antibiotic.</p>1<p>DS, commercial defibrinated wool sheep blood; DH, defibrinated hair sheep blood; CH, citrated hair sheep blood.</p>2<p>P, penicillin G 10 U; Cro, ceftriaxone 30 µg; CC, clindamycin 2 µg; E, erythromycin 15 µg; CIP, ciprofloxacin 5 µg; M, meropenem 10 µg; D, doxycycline 30 µg; LVX, levofloxacin 5 µg; SXT, sulfamethoxazole-trimethoprim 1.25 µg/23.75 µg.</p>3<p>S, sensitive; R, resistant; I, indeterminate; NA, no interpretation available.</p

Identification of bacteria by specialized microbiological tests.

<p>(A) The CAMP test for identification of Group B streptococcus (horizontal streak, GBS) demonstrates an arrowhead shaped area of enhanced hemolysis when grown near <i>S. aureus</i> (vertical streak, SA). (B) The reverse CAMP test for identification of <i>Arcanobacterium haemolyticum</i> demonstrates an indentation in the linear area of hemolysis by <i>S. aureus</i> (vertical streak, SA) when it grows adjacent to <i>A. haemolyticum</i> (horizontal streak, AH). (C) The satellite test for identification of <i>Haemophilus influenzae</i> demonstrates growth of the organisms as small satellite colonies (arrowhead, H. flu) adjacent to <i>S. aureus</i> (vertical streak, SA). Similar satellite colony formation around <i>S. aureus</i> was seen for <i>Abiotrophia defectiva</i>. Similar results were seen on both defibrinated and citrated hair sheep blood agar; results are shown on citrated hair sheep blood agar plates.</p

<i>Leptospira</i> C_T values in the Lepto-MD assay for patients with recorded day of disease information.

<p><i>Leptospira</i> C_T values in the Lepto-MD assay for patients with recorded day of disease information.</p

Leptospirosis cases and recorded rainfall in Rio de Janeiro by study month.

<p>(A) Leptospirosis cases diagnosed by RT-PCR (blue), MAT (maroon), or both (purple) are displayed by study month. MAT results are shown for all samples from 2008. (B) Rainfall for 2008 (black circles and line) and the average rainfall for the years 2003–2013 (red triangles and line).</p

Patient characteristics associated with 478 samples that tested positive and negative for <i>Leptospira</i>.

<p>Abbreviations: SD, standard deviation</p><p>¹ 65 samples tested positive for <i>Leptospira</i> in the Lepto-MD assay and/or by MAT; 3 samples tested positive by both methods.</p><p>Patient characteristics associated with 478 samples that tested positive and negative for <i>Leptospira</i>.</p

Reference <i>Leptospira</i> isolates tested with the pathogenic and reference 16S rtPCRs.

<p>Reference <i>Leptospira</i> isolates tested with the pathogenic and reference 16S rtPCRs.</p

Reported clinical data for 65 samples from patients with suspected leptospirosis.

1<p>Includes nausea, vomiting, abdominal pain, diarrhea, anorexia, and hemorrhage.</p>2<p>Includes cough, shortness of breath, and hemoptysis.</p><p>Reported clinical data for 65 samples from patients with suspected leptospirosis.</p

Pairwise comparisons of <i>Leptospira</i> PCR diagnostics.

<p>Comparison of the pathogenic <i>rt</i>PCR with the UFI assay, reference 16S rtPCR, conventional PCRs for <i>flaB/lipL41</i>, and a composite reference that takes into account <i>flaB/lipL41</i> and the reference 16S rtPCR. Samples that tested positive by at least one of these assays were considered positive, while those that tested negative by both assays were considered negative for this composite reference. Samples that tested negative in the pathogenic rtPCR had C_T values of 34.77, 35.26, and 36.11 in the UFI assay.</p><p>Pairwise comparisons of <i>Leptospira</i> PCR diagnostics.</p

Amplicon sequencing results and C_T values for select clinical samples.

1<p>Given the highly conserved nature of this region, final species determinations cannot be made from amplicon sequences.</p><p>Amplicon sequencing results and C_T values for select clinical samples.</p