Phylogenetic Analysis Reveals Source Attribution Patterns for Campylobacter spp. in Tennessee and Pennsylvania.

Campylobacteriosis is the most common bacterial foodborne illness in the United States and is frequently associated with foods of animal origin. The goals of this study were to compare clinical and non-clinical Campylobacter populations from Tennessee (TN) and Pennsylvania (PA), use phylogenetic relatedness to assess source attribution patterns, and identify potential outbreak clusters. Campylobacter isolates studied (n = 3080) included TN clinical isolates collected and sequenced for routine surveillance, PA clinical isolates collected from patients at the University of Pennsylvania Health System facilities, and non-clinical isolates from both states for which sequencing reads were available on NCBI. Phylogenetic analyses were conducted to categorize isolates into species groups and determine the population structure of each species. Most isolates were C. jejuni (n = 2132, 69.2%) and C. coli (n = 921, 29.9%), while the remaining were C. lari (0.4%), C. upsaliensis (0.3%), and C. fetus (0.1%). The C. jejuni group consisted of three clades; most non-clinical isolates were of poultry (62.7%) or cattle (35.8%) origin, and 59.7 and 16.5% of clinical isolates were in subclades associated with poultry or cattle, respectively. The C. coli isolates grouped into two clades; most non-clinical isolates were from poultry (61.2%) or swine (29.0%) sources, and 74.5, 9.2, and 6.1% of clinical isolates were in subclades associated with poultry, cattle, or swine, respectively. Based on genomic similarity, we identified 42 C. jejuni and one C. coli potential outbreak clusters. The C. jejuni clusters contained 188 clinical isolates, 19.6% of the total C. jejuni clinical isolates, suggesting that a larger proportion of campylobacteriosis may be associated with outbreaks than previously determined.

Prevalence of IgG antibodies against the severe acute respiratory syndrome coronavirus-2 among healthcare workers in Tennessee during May and June, 2020.

SARS-CoV-2 seroprevalence was low (<1%) in this large population of healthcare workers (HCWs) across the state of Tennessee (n=11,787) in May-June 2020. Among those with PCR results, 81.5% of PCR and antibody test results were concordant. SARS-CoV-2 seroprevalence was higher among HCWs working in high-community-transmission regions and among younger workers. IMPORTANCE: These results may be seen as a baseline assessment of SARS-CoV-2 seroprevalence among HCWs in the American South during a period of growth, but not yet saturation, of infections among susceptible populations. In fact, this period of May-June 2020 was marked by the extension of renewed and sustained community-wide transmission after mandatory quarantine periods expired in several more populous regions of Tennessee. Where community transmission remains low, HCWs may still be able to effectively mitigate SARS-CoV-2 transmission, preserving resources for populations at high risk of severe disease, and these sorts of data help highlight such strategies.

Expanding U.S. Laboratory Capacity for Neisseria gonorrhoeae Antimicrobial Susceptibility Testing and Whole-Genome Sequencing through the CDC's Antibiotic Resistance Laboratory Network.

U.S. gonorrhea rates are rising, and antibiotic-resistant Neisseria gonorrhoeae (AR-Ng) is an urgent public health threat. Since implementation of nucleic acid amplification tests for N. gonorrhoeae identification, the capacity for culturing N. gonorrhoeae in the United States has declined, along with the ability to perform culture-based antimicrobial susceptibility testing (AST). Yet AST is critical for detecting and monitoring AR-Ng. In 2016, the CDC established the Antibiotic Resistance Laboratory Network (AR Lab Network) to shore up the national capacity for detecting several resistance threats including N. gonorrhoeae AR-Ng testing, a subactivity of the CDC's AR Lab Network, is performed in a tiered network of approximately 35 local laboratories, four regional laboratories (state public health laboratories in Maryland, Tennessee, Texas, and Washington), and the CDC's national reference laboratory. Local laboratories receive specimens from approximately 60 clinics associated with the Gonococcal Isolate Surveillance Project (GISP), enhanced GISP (eGISP), and the program Strengthening the U.S. Response to Resistant Gonorrhea (SURRG). They isolate and ship up to 20,000 isolates to regional laboratories for culture-based agar dilution AST with seven antibiotics and for whole-genome sequencing of up to 5,000 isolates. The CDC further examines concerning isolates and monitors genetic AR markers. During 2017 and 2018, the network tested 8,214 and 8,628 N. gonorrhoeae isolates, respectively, and the CDC received 531 and 646 concerning isolates and 605 and 3,159 sequences, respectively. In summary, the AR Lab Network supported the laboratory capacity for N. gonorrhoeae AST and associated genetic marker detection, expanding preexisting notification and analysis systems for resistance detection. Continued, robust AST and genomic capacity can help inform national public health monitoring and intervention.

Emergence of Neisseria gonorrhoeae Strains Harboring a Novel Combination of Azithromycin-Attenuating Mutations.

The nimbleness of Neisseria gonorrhoeae to evade the effect of antibiotics has perpetuated the fight against antibiotic-resistant gonorrhea for more than 80 years. The ability to develop resistance to antibiotics is attributable to its indiscriminate nature in accepting and integrating exogenous DNA into its genome. Here, we provide data demonstrating a novel combination of the 23S rRNA A2059G mutation with a mosaic-multiple transferable resistance (mosaic-mtr) locus haplotype in 14 N. gonorrhoeae isolates with high-level azithromycin MICs (≥256 µg/ml), a combination that may confer more fitness than in previously identified isolates with high-level azithromycin resistance. To our knowledge, this is the first description of N. gonorrhoeae strains harboring this novel combination of resistance determinants. These strains were isolated at two independent jurisdictions participating in the Gonococcal Isolate Surveillance Project (GISP) and in the Strengthening the U.S. Response to Resistant Gonorrhea (SURRG) project. The data suggest that the genome of N. gonorrhoeae continues to shuffle its genetic material. These findings further illuminate the genomic plasticity of N. gonorrhoeae, which allows this pathogen to develop mutations to escape the inhibitory effects of antibiotics.

Is there evidence of the new variant Chlamydia trachomatis in the United States?

A specific real-time polymerase chain reaction followed by melt curve analysis was developed for the detection of the Swedish variant (nvCT) strain of Chlamydia trachomatis (CT). Surveillance was performed on 476 CT-positive clinical specimens obtained from 15 laboratories around the United States using nucleic acid amplification test assays, which would not miss the nvCT. All were negative for nvCT; thus, there is no evidence of the nvCT in the United States.

Survey of sexually transmitted disease laboratory methods in US Army laboratories.

BACKGROUND: Sexually transmitted diseases, in particular Chlamydia trachomatis and Neisseria gonorrhoeae, are ranked as the top 2 most commonly notified disease in the US Army. Although surveillance programs are in place to capture event data, no routine STD surveillance program captures laboratory test information. METHODS: To evaluate laboratory testing practices/methodologies in US Army laboratories in 2007, a questionnaire was distributed to all 38 US Army laboratories. The results of the survey were compared across Army installations to US civilian public health laboratories. RESULTS: Of 38 survey recipients, 35 (92.1%) completed the survey. Overall, 78.6% of C. trachomatis and 77.2% of N. gonorrhoeae specimens were tested by nucleic acid amplification tests. In addition, 48.6% used culture as a method of N. gonorrhoeae testing. Testing for genital herpes, trichomonas, bacterial vaginosis, syphilis, human papillomavirus, and/or premalignant/malignant cervical cells was performed by 33 of the 35 laboratories. CONCLUSIONS: A high proportion of US Army laboratories are using NAAT technology for C. trachomatis and N. gonorrhoeae testing. A more comprehensive questionnaire may be needed to accurately describe the type and volume of other STD tests. Despite the difference in survey data acquisition between the US civilian public health laboratory survey and the US Army laboratory survey, broad comparisons such as test types were able to be made. Future surveys should be extended to other US military services and should include both civilian and military laboratories.

Testing for sexually transmitted diseases in U.S. Public health laboratories in 2004.

OBJECTIVE: Appropriate laboratory testing practices are a critical part of sexually transmitted disease (STD) control. GOAL: The goal of this study was to describe the type and volume of STD tests performed in public health laboratories in the United States in 2004. STUDY DESIGN: A web-based survey was made available to 144 members of the Association of Public Health Laboratories. RESULTS: One hundred fourteen laboratories responded (79%). Overall, 3,553,196 chlamydia tests and 3,461,151 gonorrhea tests were performed; 64.4% of chlamydia tests and 60.8% of gonorrhea tests were nucleic acid amplification tests. Ninety-four percent of laboratories performed syphilis testing. Few laboratories used type-specific tests for herpes simplex virus or used new tests for trichomoniasis, bacterial vaginosis, or human papillomavirus. CONCLUSIONS: This survey collected important data that can be used to monitor trends in STD testing practices in public health laboratories.

Laboratory tests used in US public health laboratories for sexually transmitted diseases, 2000.

BACKGROUND AND OBJECTIVES: Public health laboratories are a critical component of sexually transmitted disease (STD) control in the United States. GOAL: The goal of this study was to describe the types and volume of STD tests performed in U.S. public health laboratories in 2000. STUDY DESIGN: A survey was mailed to 123 members of the Association of Public Health Laboratories. RESULTS: Eighty-one percent of 100 laboratories responded. Overall, 3294739 chlamydia tests and 3088142 gonorrhea tests were done; 62.4% of chlamydia tests and 63.6% of gonorrhea tests were DNA probes. Fifty-six percent of laboratories performed rapid plasma reagin (RPR) tests and 55% performed Venereal Disease Research Laboratory (VDRL) tests; the number of RPR tests performed was twice that of VDRL tests. Few laboratories used new technologies for bacterial vaginosis and trichomoniasis. Eighteen percent of laboratories performed herpes simplex virus serology; however, most used inaccurate tests. No laboratories performed human papillomavirus tests. CONCLUSIONS: This survey documents for the first time STD tests performed in U.S. public health laboratories.

Screening tests to detect Chlamydia trachomatis and Neisseria gonorrhoeae infections--2002.

Since publication of CDC's 1993 guidelines (CDC, Recommendations for the prevention and management of Chlamydia trachomatis infections, 1993. MMWR 1993;42[No. RR-12]:1-39), nucleic acid amplification tests (NAATs) have been introduced as critical new tools to diagnose and treat C. trachomatis and Neisseria gonorrhoeae infections. NAATs for C. trachomatis are substantially more sensitive than previous tests. When using a NAAT, any sacrifice in performance when urine is substituted for a traditional swab specimen is limited, thus reducing dependence on invasive procedures and expanding the venues where specimens can be obtained. NAATs can also detect both C. trachomatis and N. gonorrhoeae organisms in the same specimen. However, NAATs are usually more expensive than previous tests, making test performance from an economic perspective a key consideration. This report updates the 1993 guidelines for selecting laboratory tests for C. trachomatis with an emphasis on screening men and women in the United States. (In this report, screening refers to testing persons in the absence of symptoms or signs indicating C. trachomatis or N. gonorrhoeae infection.) In addition, these guidelines consider tests from an economic perspective and expand the previous guidelines to address detection of N. gonorrhoeae as well as C. trachomatis infections. Because of the increased cost of NAATs, certain laboratories are modifying manufacturers' procedures to improve test sensitivity without incurring the full cost associated with screening with a NAAT. Such approaches addressed in these guidelines are pooling of specimens before testing with a NAAT and additional testing of specimens whose non-NAAT test result is within a gray zone. This report also addresses the need for additional testing after a positive screening test to improve the specificity of a final diagnosis. To prepare these guidelines, CDC staff identified pertinent concerns, compiled the related literature published during 1990 or later, prepared tables of evidence, and drafted recommendations. Consultants, selected for their expertise or disciplinary and organizational affiliations, reviewed the draft recommendations. These final guidelines are the recommendations of CDC staff who considered contributions from scientific consultants. These guidelines are intended for laboratorians, clinicians, and managers who must choose among the multiple available tests, establish standard operating procedures for collecting and processing specimens, interpret test results for laboratory reporting, and counsel and treat patients.