The ongoing TRUST (Tracking Resistance in the United States Today) study, which began monitoring antimicrobial resistance among respiratory pathogens in 1996, routinely tracks resistance at national and regional levels. The 1999-2000 TRUST study analyzed 9499 Streptococcus pneumoniae, 1934 Haemophilus influenzae, and 1108 Moraxella catarrhalis isolates that were prospectively collected from 239 laboratories across the 9 US Bureau of the Census regions. Penicillin-resistant S. pneumoniae varied significantly by region, from 8.3% to 24.8% (P<.001). In each region, penicillin resistance closely predicted resistance to other beta-lactams, macrolides, and trimethoprim-sulfamethoxazole. Levofloxacin resistance was 0.5% nationally (regional range, 0.1%-1.0%). Multidrug resistance also varied significantly (P<.001) by region. beta-Lactamase production among H. influenzae varied significantly (regional range, 24.0%-34.6%) and M. catarrhalis (86.2%-96.8%) also varied by region. Notable variation in regional antimicrobial resistance rates (S. pneumoniae) and beta-lactamase production (H. influenzae, M. catarrhalis) exists throughout the United States.

To identify factors associated with antimicrobial resistance, data were analyzed from 27,828 isolates of Streptococcus pneumoniae submitted to the Tracking Resistance in the United States Today (TRUST) surveillance program during 4 consecutive respiratory seasons. From the 1998-1999 season to the 2001-2002 season, the prevalence of azithromycin resistance increased by 4.8% to 27.5%, the prevalence of penicillin resistance increased by 3.7% to 18.4%, the prevalence of ceftriaxone resistance increased by 0.5% to 1.7%, and the prevalence of levofloxacin resistance increased by 0.3% to 0.9%. Isolates recovered from patients <18 years of age and lower respiratory tract specimens had elevated rates of penicillin, azithromycin, and trimethoprim-sulfamethoxazole resistance (P<.00001); penicillin resistance correlated with coresistance to trimethoprim-sulfamethoxazole (87.3%), azithromycin (76.3%), ceftriaxone (9.1%), and levofloxacin (1.3%) (P<.00001). Only 62 (0.2%) of 27,828 isolates were concurrently resistant to penicillin and levofloxacin. Minimum inhibitory concentrations (MICs) of penicillin correlated strongly with MICs of ceftriaxone (R2=0.90), trimethoprim-sulfamethoxazole (R2=0.53), and azithromycin (R2=0.41). Patient age, specimen source, and penicillin resistance were factors associated with antimicrobial resistance, particularly for nonfluoroquinolone antimicrobial agents.

Global vaccination of children has dramatically reduced the incidence of illness and deaths from Bordetella pertussis, the causative agent of whooping cough. However, increased cases of whooping cough have recently been reported in several countries including the US. While there has been much attention given to waning immunity associated with the introduction of acellular vaccines 1 , another factor contributing to the outbreaks may be adaptation of B. pertussis to vaccine selection pressure. Pertactin (prn) is a component of acellular vaccines. Pertactin-negative variants of B. pertussis have recently been reported in clinical isolates from Japan, France and Finland. The variants from Japan and Finland had deletions or insertion sequences in the prn1 allele; the French isolates had deletions or truncations in the prn2 allele. 2,3 Pertactin mutants retain lethality in mouse models of infection and are transmissible in humans. 2 We analyzed the pertactin genes from twelve isolates of B. pertussis cultured from children hospitalized in Philadelphia during 2011-12 (Table 1). The entire coding region for pertactin was amplified and sequenced. 3,4 PFGE was performed with XbaI as the restriction enzyme. 4 The PFGE profiles were determined using the CDC database for US isolates. For Western blots, pertactin was detected using anti-69K antiserum (NIBSC#97/558) with WHO strain 18323 serving as the pertactin-positive reference strain.By Western blot, eleven of the twelve B. pertussis isolates were negative for pertactin.Sequencing revealed that four of these isolates had insertion sequence IS481 disrupting the pertactin coding region and seven had a stop codon truncating the protein. By PFGE typing, three isolates with IS481 inserted at nucleotide 1613 were identical. The seven isolates with the stop codon at amino acid position 425 were identical or >92% related. The pertactin allele in all 12 isolates was prn2; mutations were different from the pertactin-negative prn2 isolates from France. In the US, prn2 has been predominant pertactin allele since the 1990s. 5 However, multilocus sequence typing used to determine pertactin allele types would not have detected these variants, as the mutations were outside of the sequenced region.

Levofloxacin resistance in Streptococcus pneumoniae is rare, requiring at least two mutations in the quinolone resistance-determining region (QRDR) of topoisomerase IV and DNA gyrase. The prevalence of single QRDR mutations in these genes is unknown. Of 9,438 levofloxacin-susceptible pneumococci from the TRUST 4 surveillance study (1999)(2000), 528 strains (MICs of 0.5 to 2.0 g/ml) were selected for analysis. For comparison, 214 levofloxacin-susceptible strains (MICs of 0.5 to 1 g/ml) isolated between 1992 and 1996 were analyzed. Oligonucleotide probe assay and DNA sequencing were used to detect QRDR mutations leading to changes at Ser79 and Asp83 in ParC, Ser81 in GyrA, and Asp435 in ParE, the most frequently found substitutions among levofloxacin-resistant strains. Among the 1992 to 1996 isolates only one strain (levofloxacin MIC, 1 g/ml) had a mutation (Ser79 to Phe in ParC). No single mutations were found among 270 TRUST 4 strains with levofloxacin MICs of 0.5 g/ml. Among 244 strains for which levofloxacin MICs were 1 g/ml, 15 strains (6.1%) had a parC mutation and 3 strains (1.2%) had a parE mutation. Of 14 strains for which levofloxacin MICs were 2 g/ml, 10 strains (71%) had a parC mutation; no parE mutations were found. No gyrA mutations were detected. It was estimated that 4.5% of the 9,438 levofloxacin-susceptible TRUST 4 isolates (MICs, <0.06 to 2 g/ml) had a single parC or parE QRDR mutation. Although there has been an increase in the prevalence of single-step mutants, the increase may have been overestimated due in part to differences in geographical distribution for the two sets of isolates.

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